# qmmm (c47b2)

Combined Quantum and Molecular Mechanical Hamiltonian

A combined quantum (QM) and molecular (MM) mechanical potential

allows for the study of condensed phase chemical reactions, reactive

intermediates, and excited state isomerizations. This is necessary

since standard MM force fields are parameterized with experimental

data on the potential energy surface which may be far removed from

the region of interest, or have the wrong analytical

form. A full decription of the theory and application is given in

J. Computational Chemistry (1990) 6, 700.

The effective Hamiltonian, Heff, describes the energy and forces on

each atom. It is treated as a sum of four terms, Hqm, Hmm, Hqm/mm,

and Hbrdy.

Hqm Describes the quantum mechanical particles. The semi-

empirical methods available are AM1, PM3 and MNDO. All treat

hydrogen, first row elements plus silicon, phosphorus,

sulfur, and the halogens. MNDO has additional parameters

for aluminium, phosphorus, chromium, germanium, tin, mercury,

and lead. Full details concerning these theoretical methods

can be found in Dewar's original papers, JACS (1985) 107,

3902, JACS (1977) 99, 4899, Theoret. Chim. Acta. (1977) 46, 89.

Hmm The molecular mechanical Hamiltonian is independent of the

coordinates of the electrons and nuclei of the QM atoms.

CHARMM22 is used to treat atoms in this region.

Hqm/mm The combined Hamiltonian describes how QM and MM atoms

interact. This is composed of two electrostatic and one

van der Waals terms. Each MM atom interacts with both the

electrons and nuclei of the QM atoms (therefore two terms).

The van der Waals term is necessary since some MM atoms

possess no charge and would consequently be invisible to

the QM atoms, and in other cases often provide the only

difference in the interaction (Cl vs. Br).

Hbrdy The usual periodic or stochastic boundary conditions are

implemented.

The quantum mechanical package MOPAC 4.0 was interfaced with

Academy. There are several limitations with the current program

implemntation. The current plan is to update the quantum mechanical

procedures to MOPAC 6.0, to include vibrational analysis using

analytical functions, with the possibility of using free energy

perturbation.

1) QUANTUM module

* Syntax | Syntax of QM/MM Commands

* Description | Brief Description of Quantum Commands

* GLINK | GHO Method and GLNK Command

* DECO | DECO Command

* DAMP | DAMP Command

* PERT | PERT Command

* pBOUNd | Simple Periodic Boundary Condition

* GROUp | GROUp keyword

* CHDYn | CHDYn keyword

* NEWD | NEWDS Command

* EXTE | EXTErnal File Command

* LEPS | LEPS Command

* SVB | SVB Command

* 2DSVB | 2D Usage of SVB

2) SQUANTM module

* SQUANTUM | SQUANTUM Module

* SQM_Syntax | Syntax of the SQUANTM commands

* SQM_Install | Installation of SQUANTM in CHARMM environment

A combined quantum (QM) and molecular (MM) mechanical potential

allows for the study of condensed phase chemical reactions, reactive

intermediates, and excited state isomerizations. This is necessary

since standard MM force fields are parameterized with experimental

data on the potential energy surface which may be far removed from

the region of interest, or have the wrong analytical

form. A full decription of the theory and application is given in

J. Computational Chemistry (1990) 6, 700.

The effective Hamiltonian, Heff, describes the energy and forces on

each atom. It is treated as a sum of four terms, Hqm, Hmm, Hqm/mm,

and Hbrdy.

Hqm Describes the quantum mechanical particles. The semi-

empirical methods available are AM1, PM3 and MNDO. All treat

hydrogen, first row elements plus silicon, phosphorus,

sulfur, and the halogens. MNDO has additional parameters

for aluminium, phosphorus, chromium, germanium, tin, mercury,

and lead. Full details concerning these theoretical methods

can be found in Dewar's original papers, JACS (1985) 107,

3902, JACS (1977) 99, 4899, Theoret. Chim. Acta. (1977) 46, 89.

Hmm The molecular mechanical Hamiltonian is independent of the

coordinates of the electrons and nuclei of the QM atoms.

CHARMM22 is used to treat atoms in this region.

Hqm/mm The combined Hamiltonian describes how QM and MM atoms

interact. This is composed of two electrostatic and one

van der Waals terms. Each MM atom interacts with both the

electrons and nuclei of the QM atoms (therefore two terms).

The van der Waals term is necessary since some MM atoms

possess no charge and would consequently be invisible to

the QM atoms, and in other cases often provide the only

difference in the interaction (Cl vs. Br).

Hbrdy The usual periodic or stochastic boundary conditions are

implemented.

The quantum mechanical package MOPAC 4.0 was interfaced with

Academy. There are several limitations with the current program

implemntation. The current plan is to update the quantum mechanical

procedures to MOPAC 6.0, to include vibrational analysis using

analytical functions, with the possibility of using free energy

perturbation.

1) QUANTUM module

* Syntax | Syntax of QM/MM Commands

* Description | Brief Description of Quantum Commands

* GLINK | GHO Method and GLNK Command

* DECO | DECO Command

* DAMP | DAMP Command

* PERT | PERT Command

* pBOUNd | Simple Periodic Boundary Condition

* GROUp | GROUp keyword

* CHDYn | CHDYn keyword

* NEWD | NEWDS Command

* EXTE | EXTErnal File Command

* LEPS | LEPS Command

* SVB | SVB Command

* 2DSVB | 2D Usage of SVB

2) SQUANTM module

* SQUANTUM | SQUANTUM Module

* SQM_Syntax | Syntax of the SQUANTM commands

* SQM_Install | Installation of SQUANTM in CHARMM environment

Top

Syntax for QUANTUM commands

QUANtum [atom-selection] [GLNK atom-selection] [LEPS int1 int2 int3]

[DECO]

[PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT]

[NGUEss int]

[NEWD int] ewald-spec

[IFIL int] [ITRMax int]

[CAMP] [KING] [PULAy]

[SHIFt real] [SCFCriteria real]

[UHF] [C.I.] [EXCIted] [NMOS int] [MICR int]

[TRIPLET|QUARTET|QUINTET|SEXTET]

[AM1|PM3|MNDO] [CHARge int] [NOCUtoff]

[ALPM real] [RHO0 real] [SFT1 real]

[EXCIted] [BIRADical] [C.I.]

[ITER] [EIG2] [ENERGY] [ PL ]

[DEBUG [1ELEC] [DENSITY] [FOCK] [VECTor]]

[LEPS LEPA int LEPB int LEPC int

D1AB real D1BC real D1AC real

R1AB real R1BC real R1AC real

B1AB real B1BC real B1AC real

S1AB real S1BC real S1AC real

D2AB real D2BC real D2AC real

R2AB real R2BC real R2AC real

B2AB real B2BC real B2AC real

S2AB real S2BC real S2AC real]

ewald-spec::= { [ KMAX integer ] } KSQMAX integer

{ KMXX integer KMXY integer KMXZ integer }

MULLiken

ADDLinkatom link-atom-name atom-spec atom-spec

RELLinkatom link-atom-name atom-spec atom-spec

link-atom-name ::= a four character descriptor starting with QQ.

atom-spec::= {residue-number atom-name}

{ segid resid atom-name }

{ BYNUm atom-number }

Syntax for QUANTUM commands

QUANtum [atom-selection] [GLNK atom-selection] [LEPS int1 int2 int3]

[DECO]

[PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT]

[NGUEss int]

[NEWD int] ewald-spec

[IFIL int] [ITRMax int]

[CAMP] [KING] [PULAy]

[SHIFt real] [SCFCriteria real]

[UHF] [C.I.] [EXCIted] [NMOS int] [MICR int]

[TRIPLET|QUARTET|QUINTET|SEXTET]

[AM1|PM3|MNDO] [CHARge int] [NOCUtoff]

[ALPM real] [RHO0 real] [SFT1 real]

[EXCIted] [BIRADical] [C.I.]

[ITER] [EIG2] [ENERGY] [ PL ]

[DEBUG [1ELEC] [DENSITY] [FOCK] [VECTor]]

[LEPS LEPA int LEPB int LEPC int

D1AB real D1BC real D1AC real

R1AB real R1BC real R1AC real

B1AB real B1BC real B1AC real

S1AB real S1BC real S1AC real

D2AB real D2BC real D2AC real

R2AB real R2BC real R2AC real

B2AB real B2BC real B2AC real

S2AB real S2BC real S2AC real]

ewald-spec::= { [ KMAX integer ] } KSQMAX integer

{ KMXX integer KMXY integer KMXZ integer }

MULLiken

ADDLinkatom link-atom-name atom-spec atom-spec

RELLinkatom link-atom-name atom-spec atom-spec

link-atom-name ::= a four character descriptor starting with QQ.

atom-spec::= {residue-number atom-name}

{ segid resid atom-name }

{ BYNUm atom-number }

Top

Description of QUANtum Commands

Most keywords preceed an equal sign followed by an appropriate

value. A description of each is given below.

1ELECtron The final one-electron matrix is printed out. This matrix

is composed of atomic orbitals; the array element between

orbitals i and j on different atoms is given by,

H(i,j) = 0.5 (beta(i) + beta(j)(overlap(i,j))

The matrix elements between orbitals i and j on the same

atom are calculated from the electron-nuclear attraction

energy, and also from the U(i) value if i=j.

The one-electron matrix is unaffected by (a) the charge and

(b) the electron density. It is only a function of the

geometry. Abbreviation: 1ELEC.

0SCF The data can be read in and output, but no actual

calculation is performed when this keyword is used.

This is useful as a check on the input data.

All obvious errors are trapped, and warning messages printed.

A second use is to convert from one format to another.

The input geometry is printed in various formats at the

end of a 0SCF calculation. If NOINTER is absent, cartesian

coordinates are printed.

Unconditionally, MOPAC Z-matrix internal coordinates are

printed, and if AIGOUT is present, Gaussian Z-matrix

internal coordinates are printed. 0SCF should now be used

in place of DDUM.

1SCF When users want to examine the results of a single SCF

calculation of a geometry, 1SCF should be used. 1SCF can

be used in conjunction with RESTART, in which case a single

SCF calculation will be done, and the results printed.

When 1SCF is used on its own (that is, RESTART is not also

used) then derivatives will only be calculated if GRAD is

also specified. 1SCF is helpful in a learning situation.

MOPAC normally performs many SCF calculations, and in

order to minimize output when following the working of the

SCF calculation, 1SCF is very useful.

AM1 The AM1 method is to be used. By default MNDO is run.

PM3 The PM3 method is to be used. By default MNDO is run.

NOCUtoff QM/MM cutoffs are disabled, such that the QM region

interacts with all MM charges. By default the QM region

only interacts with those charges that are within the

standard CHARMM nonbond cutoffs.

ANALYTical By default, finite difference derivatives of energy with

respect to geometry are used. If ANALYT is specified,

then analytical derivatives are used instead. Since the

analytical derivatives are over Gaussian functions --

a STO-6G basis set is used -- the overlaps are also over

Gaussian functions. This will result in a very small

(less than 0.1 Kcal/mole) change in heat of formation.

Use analytical derivatives (a) when the mantissa used is

less than about 51-53 bits, or (b) when comparison with

finite difference is desired. Finite difference

derivatives are still used when non-variationally optimized

wavefunctions are present.

BIRADical NOTE: BIRADICAL is a redundant keyword, and represents a

particular configuration interaction calculation.

Experienced users of MECI (q.v.) can duplicate the effect

of the keyword BIRADICAL by using the MECI keywords

OPEN(2,2) and SINGLET. For molecules which are believed to

have biradicaloid character the option exists to optimize

the lowest singlet energy state which results from the

mixing of three states. These states are, in order, (1) the

(micro)state arising from a one electron excitation from

the HOMO to the LUMO, which is combined with the microstate

resulting from the time-reversal operator acting on the

parent microstate, the result being a full singlet state;

(2) the state resulting from de-excitation from the formal

LUMO to the HOMO; and (3) the state resulting from the single

electron in the formal HOMO being excited into the LUMO.

Microstate 1 Microstate 2 Microstate 3

Alpha Beta Alpha Beta Alpha Beta Alpha Beta

LUMO * * * *

--- --- --- --- --- --- --- ---

+

HOMO * * * *

--- --- --- --- --- --- --- ---

A configuration interaction calculation is involved here.

A biradical calculation done without C.I. at the RHF

level would be meaningless. Either rotational invariance

would be lost, as in the D2d form of ethylene, or very

artificial barriers to rotations would be found, such as in

a methane molecule "orbiting" a D2d ethylene. In both

cases the inclusion of limited configuration interaction

corrects the error. BIRADICAL should not be used if

either the HOMO or LUMO is degenerate; in

this case, the full manifold of HOMO x LUMO should be

included in the C.I., using MECI options. The user should

be aware of this situation. When the biradical

calculation is performed correctly, the result is normally

a net stabilization. However, if the first singlet

excited state is much higher in energy than the

closed-shell ground state, BIRADICAL can lead to a

destabilization. Abbreviation: BIRAD. See also MECI,

C.I., OPEN, SINGLET.

CAMKINg

CHARge When the system being studied is an ion, the charge, n, on

the ion must be supplied by CHARGE=n. For cations n can be

1 or 2 or 3, etc, for anions -1 or -2 or -3, etc.

EXAMPLES

ION KEYWORD ION KEYWORD

NH4(+) CHARGE=1 CH3COO(-) CHARGE=-1

C2H5(+) CHARGE=1 (COO)(=) CHARGE=-2

SO4(=) CHARGE=-2 PO4(3-) CHARGE=-3

HSO4(-) CHARGE=-1 H2PO4(-) CHARGE=-1

C.I. Normally configuration interaction is invoked if any of the

keywords which imply a C.I. calculation are used, such as

BIRADICAL, TRIPLET or QUARTET. Note that ROOT= does not

imply a C.I. calculation: ROOT= is only used when a C.I.

calculation is done. However, as these implied C.I.'s

involve the minimum number of configurations practical,

the user may want to define a larger than minimum C.I., in

which case the keyword C.I.=n can be used. When C.I.=n is

specified, the n M.O.'s which "bracket" the occupied-

virtual energy levels will be used. Thus, C.I.=2 will

include both the HOMO and the LUMO, while C.I.=1 (implied

for odd-electron systems) will only include the HOMO

(This will do nothing for a closed-shell system, and leads

to Dewar's half-electron correction for odd-electron

systems). Users should be aware of the rapid increase

in the size of the C.I. with increasing numbers of M.O.'s

being used. Numbers of microstates implied by the use of

the keyword C.I.=n on its own are as follows:

Keyword Even-electron systems Odd-electron systems

No. of electrons, configs No. of electrons, configs

Alpha Beta Alpha Beta

C.I.=1 1 1 1 1 0 1

C.I.=2 1 1 4 1 0 2

C.I.=3 2 2 9 2 1 9

C.I.=4 2 2 36 2 1 24

C.I.=5 3 3 100 3 2 100

C.I.=6 3 3 400 3 2 300

C.I.=7 4 4 1225 4 3 1225

C.I.=8 (Do not use unless other keywords also used, see below)

If a change of spin is defined, then larger numbers of

M.O.'s can be used up to a maximum of 10. The C.I. matrix

is of size 100 x 100. For calculations involving up to 100

configurations, the spin-states are exact eigenstates of

the spin operators. For systems with more than 100

configurations, the 100 configurations of lowest energy are

used. See also MICROS and the keywords defining spin-states.

Note that for any system, use of C.I.=5 or higher normally

implies the diagonalization of a 100 by 100 matrix. As a

geometry optimization using a C.I. requires the derivatives

to be calculated using derivatives of the C.I. matrix,

geometry optimization with large C.I.'s will require more

time than smaller C.I.'s.

Associated keywords: MECI, ROOT=, MICROS, SINGLET, DOUBLET, etc.

C.I.=(n,m) In addition to specifying the number of M.O.'s in the

active space, the number of electrons can also be defined.

In C.I.=(n,m), n is the number of M.O.s in the active

space, and m is the number of doubly filled levels to be used.

EXAMPLES

Keywords Number of M.O.s No. Electrons

C.I.=2 2 2 (1)

C.I.=(2,1) 2 2 (3)

C.I.=(3,1) 3 2 (3)

C.I.=(3,2) 3 4 (5)

C.I.=(3,0) OPEN(2,3) 3 2 (N/A)

C.I.=(3,1) OPEN(2,2) 3 4 (N/A)

C.I.=(3,1) OPEN(1,2) 3 N/A (3)

Odd electron systems given in parentheses.

DEBUG Certain keywords have specific output control meanings, such as

FOCK, VECTORS and DENSITY. If they are used, only the final

arrays of the relevant type are printed. If DEBUG is supplied,

then all arrays are printed. This is useful in debugging

ITER. DEBUG can also increase the amount of output produced

when certain output keywords are used, e.g. COMPFG.

DCART The cartesian derivatives which are calculated in DCART for

variationally optimized systems are printed if the keyword

DCART is present. The derivatives are in units of

kcals/Angstrom, and the coordinates are displacements

in x, y, and z.

DENSITY At the end of a job, when the results are being printed,

the density matrix is also printed. For RHF the normal

density matrix is printed. For UHF the sum of the alpha

and beta density matrices is printed.

If density is not requested, then the diagonal of the

density matrix, i.e., the electron density on the atomic

orbitals, will be printed.

DOUBLet When a configuration interaction calculation is done,

all spin states are calculated simultaneously, either

for component of spin = 0 or 1/2. When only doublet states

are of interest, then DOUBLET can be specified, and all

other spin states, while calculated, are ignored in the

choice of root to be used.

Note that while almost every odd-electron system will have

a doublet ground state, DOUBLET should still be specified

if the desired state must be a doublet.

DOUBLET has no meaning in a UHF calculation.

EIGS

EIG2

ENERGY

ESR The unpaired spin density arising from an odd-electron

system can be calculated both RHF and UHF. In a UHF

calculation the alpha and beta M.O.'s have different

spatial forms, so unpaired spin density can naturally

be present on in-plane hydrogen atoms such as in the phenoxy

radical.

In the RHF formalism a MECI calculation is performed. If the

keywords OPEN and C.I.= are both absent then only a single

state is calculated. The unpaired spin density is then

calculated from the state function. In order to have

unpaired spin density on the hydrogens in, for example,

the phenoxy radical, several states should be mixed.

EXCIted The state to be calculated is the first excited open-shell

singlet state. If the ground state is a singlet, then the

state calculated will be S(1); if the ground state is a

triplet, then S(2). This state would normally be the

state resulting from a one-electron excitation from the

HOMO to the LUMO. Exceptions would be if the lowest

singlet state were a biradical, in which case the EXCITED

state could be a closed shell.

The EXCITED state will be calculated from a BIRADICAL

calculation in which the second root of the C.I. matrix is

selected. Note that the eigenvector of the C.I. matrix is

not used in the current formalism.

Abbreviation: EXCI.

NOTE: EXCITED is a redundant keyword, and represents a

particular configuration interaction calculation.

Experienced users of MECI can duplicate the effect of the

keyword EXCITED by using the MECI keywords OPEN(2,2),

SINGLET, and ROOT=2.

FOCK

FORCE A force-calculation is to be run. The Hessian, that is

the matrix (in millidynes per Angstrom) of second

derivatives of the energy with respect to displacements of

all pairs of atoms in x, y, and z directions, is

calculated. On diagonalization this gives the force

constants for the molecule. The force matrix, weighted

for isotopic masses, is then used for calculating the

vibrational frequencies. The system can be characterized

as a ground state or a transition state by the presence of

five (for a linear system) or six eigenvalues which are

very small (less than about 30 reciprocal centimeters). A

transition state is further characterized by one, and

exactly one, negative force constant.

A FORCE calculation is a prerequisite for a THERMO calculation.

Before a FORCE calculation is started, a check is made to

ensure that a stationary point is being used. This check

involves calculating the gradient norm (GNORM) and if it is

significant, the GNORM will be reduced using BFGS.

All internal coordinates are optimized, and any symmetry

constraints are ignored at this point. An implication of

this is that if the specification of the geometry relies on

any angles being exactly 180 or zero degrees, the

calculation may fail.

The geometric definition supplied to FORCE should not rely

on angles or dihedrals assuming exact values. (The test

of exact linearity is sufficiently slack that most

molecules that are linear, such as acetylene and but-2-yne,

should not be stopped.) See also THERMO, LET, TRANS,

ISOTOPE.

In a FORCE calculation, PRECISE will eliminate quartic

contamination (part of the anharmonicity). This is

normally not important, therefore PRECISE should not

routinely be used.

In a FORCE calculation, the SCF criterion is automatically

made more stringent; this is the main cause of the SCF

failing in a FORCE calculation.

ITER The default maximum number of SCF iterations is 200.

When this limit presents difficulty, ITRY=nn can be used

to re-define it. For example, if ITRY=400 is used, the

maximum number of iterations will be set to 400. ITRY

should normally not be changed until all other means of

obtaining a SCF have been exhausted, e.g. PULAY CAMP-KING etc.

INTERP

LPULAY

LARGE Most of the time the output invoked by keywords is

sufficient. LARGE will cause less-commonly wanted, but

still useful, output to be printed.

1. To save space, DRC and IRC outputs will, by default,

only print the line with the percent sign. Other output

can be obtained by use of the keyword LARGE, according to

the following rules:

Keyword Effect

LARGE Print all internal and cartesian coordinates

and cartesian velocities.

LARGE=1 Print all internal coordinates.

LARGE=-1 Print all internal and cartesian coordinates

and cartesian velocities.

LARGE=n Print every n'th set of internal coordinates.

LARGE=-n Print every n'th set of internal and cartesian

coordinates and cartesian velocities.

If LARGE=1 is used, the output will be the same as that of

Version 5.0, when LARGE was not used. If LARGE is used, the

output will be the same as that of Version 5.0, when LARGE

was used. To save disk space, do not use LARGE.

MECI At the end of the calculation details of the Multi Electron

Configuration Interaction calculation are printed if MECI

is specified. The state vectors can be printed by

specifying VECTORS. The MECI calculation is either

invoked automatically, or explicitly invoked by the use of

the C.I.=n keyword.

MICRos The microstates used by MECI are normally generated by use

of a permutation operator. When individually defined

microstates are desired, then MICROS=n can be used, where

n defines the number of microstates to be read in.

Format for Microstates

After the geometry data plus any symmetry data are read in,

data defining each microstate is read in, using format

20I1, one microstate per line. The microstate data is

preceded by the word "MICROS" on a line by itself. There

is at present no mechanism for using MICROS with a reaction path.

For a system with n M.O.'s in the C.I. (use OPEN=(n1,n) or

C.I.=n to do this), the populations of the n alpha M.O.'s

are defined, followed by the n beta M.O.'s. Allowed

occupancies are zero and one. For n=6 the closed-shell

ground state would be defined as 111000111000, meaning one

electron in each of the first three alpha M.O.'s, and one

electron in each of the first three beta M.O.'s.

Users are warned that they are responsible for completing

any spin manifolds. Thus while the state 111100110000

is a triplet state with component of spin = 1, the state

111000110100, while having a component of spin = 0 is

neither a singlet nor a triplet. In order to complete the

spin manifold the microstate 110100111000 must also be included.

If a manifold of spin states is not complete, then the

eigenstates of the spin operator will not be quantized.

When and only when 100 or fewer microstates are supplied,

can spin quantization be conserved.

There are two other limitations on possible microstates.

First, the number of electrons in every microstate should

be the same. If they differ, a warning message will be

printed, and the calculation continued (but the results

will almost certainly be nonsense). Second, the component

of spin for every microstate must be the same, except for

teaching purposes. Two microstates of different

components of spin will have a zero matrix element

connecting them. No warning will be given as this is a

reasonable operation in a teaching situation. For example, if

all states arising from two electrons in two levels are to

be calculated say for teaching Russel-Saunders coupling,

then the following microstates would be used:

Microstate No. of alpha, beta electrons Ms State

1100 2 0 1 Triplet

1010 1 1 0 Singlet

1001 1 1 0 Mixed

0110 1 1 0 Mixed

0101 1 1 0 Singlet

0011 0 2 -1 Triplet

Constraints on the space manifold are just as rigorous, but

much easier to satisfy. If the energy levels are

degenerate, then all components of a manifold of degenerate

M.O.'s should be either included or excluded. If only

some, but not all, components are used, the required

degeneracy of the states will be missing.

As an example, for the tetrahedral methane cation, if the user

supplies the microstates corresponding to a component of

spin = 3/2, neglecting Jahn-Teller distortion, the minimum

number of states that can be supplied is 90 = (6!/(1!*5!))*

(6!/(4!*2!)).

While the total number of electrons should be the same for all

microstates, this number does not need to be the same as

the number of electrons supplied to the C.I.; thus in the

example above, a cationic state could be 110000111000.

The format is defined as 20I1 so that spaces can be used

for empty M.O.'s.

MNDO The default Hamiltonian within MOPAC is MNDO, with the

alternatives of AM1 and MINDO/3. To use the MINDO/3

Hamiltonian the keyword MINDO/3 should be used. Acceptable

alternatives to the keyword MINDO/3 are MINDO and MINDO3.

NGUEss The number of steps to regenerate initial guess during molecular

dynamics. The default is 100 step. If NGUEss <= 0, then it will

be used previous density all over the dynamics. Only applied in

the molecular dynamics.

PRECISE The criteria for terminating all optimizations, electronic and

geometric, are to be increased by a factor, normally, 100.

This can be used where more precise results are wanted. If

the results are going to be used in a FORCE calculation,

where the geometry needs to be known quite precisely, then

PRECISE is recommended; for small systems the extra cost in

CPU time is minimal.

PRECISE is not recommended for experienced users, instead

GNORM=n.nn and SCFCRT=n.nn are suggested. PRECISE should

only very rarely be necessary in a FORCE calculation: all

it does is remove quartic contamination, which only affects

the trivial modes significantly, and is very expensive

in CPU time.

PULAy The default converger in the SCF calculation is to be

replaced by Pulay's procedure as soon as the density matrix

is sufficiently stable. A considerable improvement in

speed can be achieved by the use of PULAY. If a large

number of SCF calculations are envisaged, a sample calculation

using 1SCF and PULAY should be compared with using 1SCF on

its own, and if a saving in time results, then PULAY should

be used in the full calculation. PULAY should be used with

care in that its use will prevent the combined package of

convergers (SHIFT, PULAY and the CAMP-KING convergers)

from automatically being used in the event that the system

fails to go SCF in (ITRY-10) iterations.

The combined set of convergers very seldom fails.

QUARTet RHF interpretation: The desired spin-state is a quartet,

i.e., the state with component of spin = 1/2 and spin =

3/2. When a configuration interaction calculation is done,

all spin states of spin equal to, or greater than 1/2 are

calculated simultaneously, for component of spin = 1/2.

From these states the quartet states are selected when

QUARTET is specified, and all other spin states, while

calculated, are ignored in the choice of root to be used.

If QUARTET is used on its own, then a single state,

corresponding to an alpha electron in each of three M.O.'s

is calculated.

UHF interpretation: The system will have three more alpha

electrons than beta electrons.

QUINTet RHF interpretation: The desired spin-state is a quintet,

that is, the state with component of spin = 0 and spin = 2.

When a configuration interaction calculation is done, all

spin states of spin equal to, or greater than 0 are

calculated simultaneously, for component of spin = 0.

From these states the quintet states are selected when

QUINTET is specified, and the septet states, while

calculated, will be ignored in the choice of root to be

used. If QUINTET is used on its own, then a single state,

corresponding to an alpha electron in each of four M.O.'s

is calculated.

UHF interpretation: The system will have three more alpha

electrons than beta electrons.

ROOT The n'th root of a C.I. calculation is to be used in the

calculation. If a keyword specifying the spin-state is

also present, e.g. SINGLET or TRIPLET, then the n'th root

of that state will be selected. Thus ROOT=3 and SINGLET

will select the third singlet root. If ROOT=3 is used on

its own, then the third root will be used, which may be a

triplet, the third singlet, or the second singlet (the

second root might be a triplet). In normal use, this

keyword would not be used. It is retained for educational

and research purposes. Unusual care should be exercised

when ROOT= is specified.

SCFCrt The default SCF criterion is to be replaced by that defined

by SCFCRT=. The SCF criterion is the change in energy in

kcal/mol on two successive iterations. Other minor

criteria may make the requirements for an SCF slightly more

stringent. The SCF criterion can be varied from about

0.001 to 1.D-25, although numbers in the range 0.0001 to

1.D-9 will suffice for most applications.

An overly tight criterion can lead to failure to achieve a

SCF, and consequent failure of the run.

SEXTet RHF interpretation: The desired spin-state is a sextet:

the state with component of spin = 1/2 and spin = 5/2.

The sextet states are the highest spin states normally

calculable using MOPAC in its unmodified form. If SEXTET

is used on its own, then a single state, corresponding to

one alpha electron in each of five M.O.'s, is calculated.

If several sextets are to be calculated, say the second

or third, then OPEN(n1,n2) should be used.

UHF interpretation: The system will have five more alpha

electrons than beta electrons.

SHIFt In an attempt to obtain an SCF by damping oscillations

which slow down the convergence or prevent an SCF being

achieved, the virtual M.O. energy levels are shifted up or

down in energy by a shift technique. The principle is that

if the virtual M.O.'s are changed in energy relative to

the occupied set, then the polarizability of the occupied

M.O.'s will change pro rata. Normally, oscillations are

due to autoregenerative charge fluctuations.

The SHIFT method has been re-written so that the value of

SHIFT changes automatically to give a critically-damped

system. This can result in a positive or negative shift

of the virtual M.O. energy levels. If a non-zero SHIFT

is specified, it will be used to start the SHIFT technique,

rather than the default 15eV. If SHIFT=0 is specified,

the SHIFT technique will not be used unless normal

convergence techniques fail and the automatic "ALL

CONVERGERS..." message is produced.

SINGLet When a configuration interaction calculation is done, all spin

states are calculated simultaneously, either for component

of spin = 0 or 1/2. When only singlet states are of

interest, then SINGLET can be specified, and all other spin

states, while calculated, are ignored in the choice of root

to be used.

Note that while almost every even-electron system will

have a singlet ground state, SINGLET should still be

specified if the desired state must be a singlet.

SINGLET has no meaning in a UHF calculation, but see also TRIPLET.

TRIPLet The triplet state is defined. If the system has an odd

number of electrons, an error message will be printed.

UHF interpretation. The number of alpha electrons exceeds

that of the beta electrons by 2. If TRIPLET is not

specified, then the numbers of alpha and beta electrons are

set equal. This does not necessarily correspond to a singlet.

RHF interpretation.

An RHF MECI calculation is performed to calculate the

triplet state. If no other C.I. keywords are used, then

only one state is calculated by default. The occupancy of

the M.O.'s in the SCF calculation is defined as

(...2,1,1,0,..), that is, one electron is put in each of

the two highest occupied M.O.'s.

See keywords C.I.=n and OPEN(n1,n2).

UHF The unrestricted Hartree-Fock Hamiltonian is to be used.

VECTors The eigenvectors are to be printed. In UHF calculations

both alpha and beta eigenvectors are printed; in all cases

the full set, occupied and virtual, are output. The

eigenvectors are normalized to unity, that is the sum of

the squares of the coefficients is exactly one. If DEBUG

is specified, then ALL eigenvectors on every iteration of

every SCF calculation will be printed. This is useful in

a learning context, but would normally be very undesirable.

Description of QUANtum Commands

Most keywords preceed an equal sign followed by an appropriate

value. A description of each is given below.

1ELECtron The final one-electron matrix is printed out. This matrix

is composed of atomic orbitals; the array element between

orbitals i and j on different atoms is given by,

H(i,j) = 0.5 (beta(i) + beta(j)(overlap(i,j))

The matrix elements between orbitals i and j on the same

atom are calculated from the electron-nuclear attraction

energy, and also from the U(i) value if i=j.

The one-electron matrix is unaffected by (a) the charge and

(b) the electron density. It is only a function of the

geometry. Abbreviation: 1ELEC.

0SCF The data can be read in and output, but no actual

calculation is performed when this keyword is used.

This is useful as a check on the input data.

All obvious errors are trapped, and warning messages printed.

A second use is to convert from one format to another.

The input geometry is printed in various formats at the

end of a 0SCF calculation. If NOINTER is absent, cartesian

coordinates are printed.

Unconditionally, MOPAC Z-matrix internal coordinates are

printed, and if AIGOUT is present, Gaussian Z-matrix

internal coordinates are printed. 0SCF should now be used

in place of DDUM.

1SCF When users want to examine the results of a single SCF

calculation of a geometry, 1SCF should be used. 1SCF can

be used in conjunction with RESTART, in which case a single

SCF calculation will be done, and the results printed.

When 1SCF is used on its own (that is, RESTART is not also

used) then derivatives will only be calculated if GRAD is

also specified. 1SCF is helpful in a learning situation.

MOPAC normally performs many SCF calculations, and in

order to minimize output when following the working of the

SCF calculation, 1SCF is very useful.

AM1 The AM1 method is to be used. By default MNDO is run.

PM3 The PM3 method is to be used. By default MNDO is run.

NOCUtoff QM/MM cutoffs are disabled, such that the QM region

interacts with all MM charges. By default the QM region

only interacts with those charges that are within the

standard CHARMM nonbond cutoffs.

ANALYTical By default, finite difference derivatives of energy with

respect to geometry are used. If ANALYT is specified,

then analytical derivatives are used instead. Since the

analytical derivatives are over Gaussian functions --

a STO-6G basis set is used -- the overlaps are also over

Gaussian functions. This will result in a very small

(less than 0.1 Kcal/mole) change in heat of formation.

Use analytical derivatives (a) when the mantissa used is

less than about 51-53 bits, or (b) when comparison with

finite difference is desired. Finite difference

derivatives are still used when non-variationally optimized

wavefunctions are present.

BIRADical NOTE: BIRADICAL is a redundant keyword, and represents a

particular configuration interaction calculation.

Experienced users of MECI (q.v.) can duplicate the effect

of the keyword BIRADICAL by using the MECI keywords

OPEN(2,2) and SINGLET. For molecules which are believed to

have biradicaloid character the option exists to optimize

the lowest singlet energy state which results from the

mixing of three states. These states are, in order, (1) the

(micro)state arising from a one electron excitation from

the HOMO to the LUMO, which is combined with the microstate

resulting from the time-reversal operator acting on the

parent microstate, the result being a full singlet state;

(2) the state resulting from de-excitation from the formal

LUMO to the HOMO; and (3) the state resulting from the single

electron in the formal HOMO being excited into the LUMO.

Microstate 1 Microstate 2 Microstate 3

Alpha Beta Alpha Beta Alpha Beta Alpha Beta

LUMO * * * *

--- --- --- --- --- --- --- ---

+

HOMO * * * *

--- --- --- --- --- --- --- ---

A configuration interaction calculation is involved here.

A biradical calculation done without C.I. at the RHF

level would be meaningless. Either rotational invariance

would be lost, as in the D2d form of ethylene, or very

artificial barriers to rotations would be found, such as in

a methane molecule "orbiting" a D2d ethylene. In both

cases the inclusion of limited configuration interaction

corrects the error. BIRADICAL should not be used if

either the HOMO or LUMO is degenerate; in

this case, the full manifold of HOMO x LUMO should be

included in the C.I., using MECI options. The user should

be aware of this situation. When the biradical

calculation is performed correctly, the result is normally

a net stabilization. However, if the first singlet

excited state is much higher in energy than the

closed-shell ground state, BIRADICAL can lead to a

destabilization. Abbreviation: BIRAD. See also MECI,

C.I., OPEN, SINGLET.

CAMKINg

CHARge When the system being studied is an ion, the charge, n, on

the ion must be supplied by CHARGE=n. For cations n can be

1 or 2 or 3, etc, for anions -1 or -2 or -3, etc.

EXAMPLES

ION KEYWORD ION KEYWORD

NH4(+) CHARGE=1 CH3COO(-) CHARGE=-1

C2H5(+) CHARGE=1 (COO)(=) CHARGE=-2

SO4(=) CHARGE=-2 PO4(3-) CHARGE=-3

HSO4(-) CHARGE=-1 H2PO4(-) CHARGE=-1

C.I. Normally configuration interaction is invoked if any of the

keywords which imply a C.I. calculation are used, such as

BIRADICAL, TRIPLET or QUARTET. Note that ROOT= does not

imply a C.I. calculation: ROOT= is only used when a C.I.

calculation is done. However, as these implied C.I.'s

involve the minimum number of configurations practical,

the user may want to define a larger than minimum C.I., in

which case the keyword C.I.=n can be used. When C.I.=n is

specified, the n M.O.'s which "bracket" the occupied-

virtual energy levels will be used. Thus, C.I.=2 will

include both the HOMO and the LUMO, while C.I.=1 (implied

for odd-electron systems) will only include the HOMO

(This will do nothing for a closed-shell system, and leads

to Dewar's half-electron correction for odd-electron

systems). Users should be aware of the rapid increase

in the size of the C.I. with increasing numbers of M.O.'s

being used. Numbers of microstates implied by the use of

the keyword C.I.=n on its own are as follows:

Keyword Even-electron systems Odd-electron systems

No. of electrons, configs No. of electrons, configs

Alpha Beta Alpha Beta

C.I.=1 1 1 1 1 0 1

C.I.=2 1 1 4 1 0 2

C.I.=3 2 2 9 2 1 9

C.I.=4 2 2 36 2 1 24

C.I.=5 3 3 100 3 2 100

C.I.=6 3 3 400 3 2 300

C.I.=7 4 4 1225 4 3 1225

C.I.=8 (Do not use unless other keywords also used, see below)

If a change of spin is defined, then larger numbers of

M.O.'s can be used up to a maximum of 10. The C.I. matrix

is of size 100 x 100. For calculations involving up to 100

configurations, the spin-states are exact eigenstates of

the spin operators. For systems with more than 100

configurations, the 100 configurations of lowest energy are

used. See also MICROS and the keywords defining spin-states.

Note that for any system, use of C.I.=5 or higher normally

implies the diagonalization of a 100 by 100 matrix. As a

geometry optimization using a C.I. requires the derivatives

to be calculated using derivatives of the C.I. matrix,

geometry optimization with large C.I.'s will require more

time than smaller C.I.'s.

Associated keywords: MECI, ROOT=, MICROS, SINGLET, DOUBLET, etc.

C.I.=(n,m) In addition to specifying the number of M.O.'s in the

active space, the number of electrons can also be defined.

In C.I.=(n,m), n is the number of M.O.s in the active

space, and m is the number of doubly filled levels to be used.

EXAMPLES

Keywords Number of M.O.s No. Electrons

C.I.=2 2 2 (1)

C.I.=(2,1) 2 2 (3)

C.I.=(3,1) 3 2 (3)

C.I.=(3,2) 3 4 (5)

C.I.=(3,0) OPEN(2,3) 3 2 (N/A)

C.I.=(3,1) OPEN(2,2) 3 4 (N/A)

C.I.=(3,1) OPEN(1,2) 3 N/A (3)

Odd electron systems given in parentheses.

DEBUG Certain keywords have specific output control meanings, such as

FOCK, VECTORS and DENSITY. If they are used, only the final

arrays of the relevant type are printed. If DEBUG is supplied,

then all arrays are printed. This is useful in debugging

ITER. DEBUG can also increase the amount of output produced

when certain output keywords are used, e.g. COMPFG.

DCART The cartesian derivatives which are calculated in DCART for

variationally optimized systems are printed if the keyword

DCART is present. The derivatives are in units of

kcals/Angstrom, and the coordinates are displacements

in x, y, and z.

DENSITY At the end of a job, when the results are being printed,

the density matrix is also printed. For RHF the normal

density matrix is printed. For UHF the sum of the alpha

and beta density matrices is printed.

If density is not requested, then the diagonal of the

density matrix, i.e., the electron density on the atomic

orbitals, will be printed.

DOUBLet When a configuration interaction calculation is done,

all spin states are calculated simultaneously, either

for component of spin = 0 or 1/2. When only doublet states

are of interest, then DOUBLET can be specified, and all

other spin states, while calculated, are ignored in the

choice of root to be used.

Note that while almost every odd-electron system will have

a doublet ground state, DOUBLET should still be specified

if the desired state must be a doublet.

DOUBLET has no meaning in a UHF calculation.

EIGS

EIG2

ENERGY

ESR The unpaired spin density arising from an odd-electron

system can be calculated both RHF and UHF. In a UHF

calculation the alpha and beta M.O.'s have different

spatial forms, so unpaired spin density can naturally

be present on in-plane hydrogen atoms such as in the phenoxy

radical.

In the RHF formalism a MECI calculation is performed. If the

keywords OPEN and C.I.= are both absent then only a single

state is calculated. The unpaired spin density is then

calculated from the state function. In order to have

unpaired spin density on the hydrogens in, for example,

the phenoxy radical, several states should be mixed.

EXCIted The state to be calculated is the first excited open-shell

singlet state. If the ground state is a singlet, then the

state calculated will be S(1); if the ground state is a

triplet, then S(2). This state would normally be the

state resulting from a one-electron excitation from the

HOMO to the LUMO. Exceptions would be if the lowest

singlet state were a biradical, in which case the EXCITED

state could be a closed shell.

The EXCITED state will be calculated from a BIRADICAL

calculation in which the second root of the C.I. matrix is

selected. Note that the eigenvector of the C.I. matrix is

not used in the current formalism.

Abbreviation: EXCI.

NOTE: EXCITED is a redundant keyword, and represents a

particular configuration interaction calculation.

Experienced users of MECI can duplicate the effect of the

keyword EXCITED by using the MECI keywords OPEN(2,2),

SINGLET, and ROOT=2.

FOCK

FORCE A force-calculation is to be run. The Hessian, that is

the matrix (in millidynes per Angstrom) of second

derivatives of the energy with respect to displacements of

all pairs of atoms in x, y, and z directions, is

calculated. On diagonalization this gives the force

constants for the molecule. The force matrix, weighted

for isotopic masses, is then used for calculating the

vibrational frequencies. The system can be characterized

as a ground state or a transition state by the presence of

five (for a linear system) or six eigenvalues which are

very small (less than about 30 reciprocal centimeters). A

transition state is further characterized by one, and

exactly one, negative force constant.

A FORCE calculation is a prerequisite for a THERMO calculation.

Before a FORCE calculation is started, a check is made to

ensure that a stationary point is being used. This check

involves calculating the gradient norm (GNORM) and if it is

significant, the GNORM will be reduced using BFGS.

All internal coordinates are optimized, and any symmetry

constraints are ignored at this point. An implication of

this is that if the specification of the geometry relies on

any angles being exactly 180 or zero degrees, the

calculation may fail.

The geometric definition supplied to FORCE should not rely

on angles or dihedrals assuming exact values. (The test

of exact linearity is sufficiently slack that most

molecules that are linear, such as acetylene and but-2-yne,

should not be stopped.) See also THERMO, LET, TRANS,

ISOTOPE.

In a FORCE calculation, PRECISE will eliminate quartic

contamination (part of the anharmonicity). This is

normally not important, therefore PRECISE should not

routinely be used.

In a FORCE calculation, the SCF criterion is automatically

made more stringent; this is the main cause of the SCF

failing in a FORCE calculation.

ITER The default maximum number of SCF iterations is 200.

When this limit presents difficulty, ITRY=nn can be used

to re-define it. For example, if ITRY=400 is used, the

maximum number of iterations will be set to 400. ITRY

should normally not be changed until all other means of

obtaining a SCF have been exhausted, e.g. PULAY CAMP-KING etc.

INTERP

LPULAY

LARGE Most of the time the output invoked by keywords is

sufficient. LARGE will cause less-commonly wanted, but

still useful, output to be printed.

1. To save space, DRC and IRC outputs will, by default,

only print the line with the percent sign. Other output

can be obtained by use of the keyword LARGE, according to

the following rules:

Keyword Effect

LARGE Print all internal and cartesian coordinates

and cartesian velocities.

LARGE=1 Print all internal coordinates.

LARGE=-1 Print all internal and cartesian coordinates

and cartesian velocities.

LARGE=n Print every n'th set of internal coordinates.

LARGE=-n Print every n'th set of internal and cartesian

coordinates and cartesian velocities.

If LARGE=1 is used, the output will be the same as that of

Version 5.0, when LARGE was not used. If LARGE is used, the

output will be the same as that of Version 5.0, when LARGE

was used. To save disk space, do not use LARGE.

MECI At the end of the calculation details of the Multi Electron

Configuration Interaction calculation are printed if MECI

is specified. The state vectors can be printed by

specifying VECTORS. The MECI calculation is either

invoked automatically, or explicitly invoked by the use of

the C.I.=n keyword.

MICRos The microstates used by MECI are normally generated by use

of a permutation operator. When individually defined

microstates are desired, then MICROS=n can be used, where

n defines the number of microstates to be read in.

Format for Microstates

After the geometry data plus any symmetry data are read in,

data defining each microstate is read in, using format

20I1, one microstate per line. The microstate data is

preceded by the word "MICROS" on a line by itself. There

is at present no mechanism for using MICROS with a reaction path.

For a system with n M.O.'s in the C.I. (use OPEN=(n1,n) or

C.I.=n to do this), the populations of the n alpha M.O.'s

are defined, followed by the n beta M.O.'s. Allowed

occupancies are zero and one. For n=6 the closed-shell

ground state would be defined as 111000111000, meaning one

electron in each of the first three alpha M.O.'s, and one

electron in each of the first three beta M.O.'s.

Users are warned that they are responsible for completing

any spin manifolds. Thus while the state 111100110000

is a triplet state with component of spin = 1, the state

111000110100, while having a component of spin = 0 is

neither a singlet nor a triplet. In order to complete the

spin manifold the microstate 110100111000 must also be included.

If a manifold of spin states is not complete, then the

eigenstates of the spin operator will not be quantized.

When and only when 100 or fewer microstates are supplied,

can spin quantization be conserved.

There are two other limitations on possible microstates.

First, the number of electrons in every microstate should

be the same. If they differ, a warning message will be

printed, and the calculation continued (but the results

will almost certainly be nonsense). Second, the component

of spin for every microstate must be the same, except for

teaching purposes. Two microstates of different

components of spin will have a zero matrix element

connecting them. No warning will be given as this is a

reasonable operation in a teaching situation. For example, if

all states arising from two electrons in two levels are to

be calculated say for teaching Russel-Saunders coupling,

then the following microstates would be used:

Microstate No. of alpha, beta electrons Ms State

1100 2 0 1 Triplet

1010 1 1 0 Singlet

1001 1 1 0 Mixed

0110 1 1 0 Mixed

0101 1 1 0 Singlet

0011 0 2 -1 Triplet

Constraints on the space manifold are just as rigorous, but

much easier to satisfy. If the energy levels are

degenerate, then all components of a manifold of degenerate

M.O.'s should be either included or excluded. If only

some, but not all, components are used, the required

degeneracy of the states will be missing.

As an example, for the tetrahedral methane cation, if the user

supplies the microstates corresponding to a component of

spin = 3/2, neglecting Jahn-Teller distortion, the minimum

number of states that can be supplied is 90 = (6!/(1!*5!))*

(6!/(4!*2!)).

While the total number of electrons should be the same for all

microstates, this number does not need to be the same as

the number of electrons supplied to the C.I.; thus in the

example above, a cationic state could be 110000111000.

The format is defined as 20I1 so that spaces can be used

for empty M.O.'s.

MNDO The default Hamiltonian within MOPAC is MNDO, with the

alternatives of AM1 and MINDO/3. To use the MINDO/3

Hamiltonian the keyword MINDO/3 should be used. Acceptable

alternatives to the keyword MINDO/3 are MINDO and MINDO3.

NGUEss The number of steps to regenerate initial guess during molecular

dynamics. The default is 100 step. If NGUEss <= 0, then it will

be used previous density all over the dynamics. Only applied in

the molecular dynamics.

PRECISE The criteria for terminating all optimizations, electronic and

geometric, are to be increased by a factor, normally, 100.

This can be used where more precise results are wanted. If

the results are going to be used in a FORCE calculation,

where the geometry needs to be known quite precisely, then

PRECISE is recommended; for small systems the extra cost in

CPU time is minimal.

PRECISE is not recommended for experienced users, instead

GNORM=n.nn and SCFCRT=n.nn are suggested. PRECISE should

only very rarely be necessary in a FORCE calculation: all

it does is remove quartic contamination, which only affects

the trivial modes significantly, and is very expensive

in CPU time.

PULAy The default converger in the SCF calculation is to be

replaced by Pulay's procedure as soon as the density matrix

is sufficiently stable. A considerable improvement in

speed can be achieved by the use of PULAY. If a large

number of SCF calculations are envisaged, a sample calculation

using 1SCF and PULAY should be compared with using 1SCF on

its own, and if a saving in time results, then PULAY should

be used in the full calculation. PULAY should be used with

care in that its use will prevent the combined package of

convergers (SHIFT, PULAY and the CAMP-KING convergers)

from automatically being used in the event that the system

fails to go SCF in (ITRY-10) iterations.

The combined set of convergers very seldom fails.

QUARTet RHF interpretation: The desired spin-state is a quartet,

i.e., the state with component of spin = 1/2 and spin =

3/2. When a configuration interaction calculation is done,

all spin states of spin equal to, or greater than 1/2 are

calculated simultaneously, for component of spin = 1/2.

From these states the quartet states are selected when

QUARTET is specified, and all other spin states, while

calculated, are ignored in the choice of root to be used.

If QUARTET is used on its own, then a single state,

corresponding to an alpha electron in each of three M.O.'s

is calculated.

UHF interpretation: The system will have three more alpha

electrons than beta electrons.

QUINTet RHF interpretation: The desired spin-state is a quintet,

that is, the state with component of spin = 0 and spin = 2.

When a configuration interaction calculation is done, all

spin states of spin equal to, or greater than 0 are

calculated simultaneously, for component of spin = 0.

From these states the quintet states are selected when

QUINTET is specified, and the septet states, while

calculated, will be ignored in the choice of root to be

used. If QUINTET is used on its own, then a single state,

corresponding to an alpha electron in each of four M.O.'s

is calculated.

UHF interpretation: The system will have three more alpha

electrons than beta electrons.

ROOT The n'th root of a C.I. calculation is to be used in the

calculation. If a keyword specifying the spin-state is

also present, e.g. SINGLET or TRIPLET, then the n'th root

of that state will be selected. Thus ROOT=3 and SINGLET

will select the third singlet root. If ROOT=3 is used on

its own, then the third root will be used, which may be a

triplet, the third singlet, or the second singlet (the

second root might be a triplet). In normal use, this

keyword would not be used. It is retained for educational

and research purposes. Unusual care should be exercised

when ROOT= is specified.

SCFCrt The default SCF criterion is to be replaced by that defined

by SCFCRT=. The SCF criterion is the change in energy in

kcal/mol on two successive iterations. Other minor

criteria may make the requirements for an SCF slightly more

stringent. The SCF criterion can be varied from about

0.001 to 1.D-25, although numbers in the range 0.0001 to

1.D-9 will suffice for most applications.

An overly tight criterion can lead to failure to achieve a

SCF, and consequent failure of the run.

SEXTet RHF interpretation: The desired spin-state is a sextet:

the state with component of spin = 1/2 and spin = 5/2.

The sextet states are the highest spin states normally

calculable using MOPAC in its unmodified form. If SEXTET

is used on its own, then a single state, corresponding to

one alpha electron in each of five M.O.'s, is calculated.

If several sextets are to be calculated, say the second

or third, then OPEN(n1,n2) should be used.

UHF interpretation: The system will have five more alpha

electrons than beta electrons.

SHIFt In an attempt to obtain an SCF by damping oscillations

which slow down the convergence or prevent an SCF being

achieved, the virtual M.O. energy levels are shifted up or

down in energy by a shift technique. The principle is that

if the virtual M.O.'s are changed in energy relative to

the occupied set, then the polarizability of the occupied

M.O.'s will change pro rata. Normally, oscillations are

due to autoregenerative charge fluctuations.

The SHIFT method has been re-written so that the value of

SHIFT changes automatically to give a critically-damped

system. This can result in a positive or negative shift

of the virtual M.O. energy levels. If a non-zero SHIFT

is specified, it will be used to start the SHIFT technique,

rather than the default 15eV. If SHIFT=0 is specified,

the SHIFT technique will not be used unless normal

convergence techniques fail and the automatic "ALL

CONVERGERS..." message is produced.

SINGLet When a configuration interaction calculation is done, all spin

states are calculated simultaneously, either for component

of spin = 0 or 1/2. When only singlet states are of

interest, then SINGLET can be specified, and all other spin

states, while calculated, are ignored in the choice of root

to be used.

Note that while almost every even-electron system will

have a singlet ground state, SINGLET should still be

specified if the desired state must be a singlet.

SINGLET has no meaning in a UHF calculation, but see also TRIPLET.

TRIPLet The triplet state is defined. If the system has an odd

number of electrons, an error message will be printed.

UHF interpretation. The number of alpha electrons exceeds

that of the beta electrons by 2. If TRIPLET is not

specified, then the numbers of alpha and beta electrons are

set equal. This does not necessarily correspond to a singlet.

RHF interpretation.

An RHF MECI calculation is performed to calculate the

triplet state. If no other C.I. keywords are used, then

only one state is calculated by default. The occupancy of

the M.O.'s in the SCF calculation is defined as

(...2,1,1,0,..), that is, one electron is put in each of

the two highest occupied M.O.'s.

See keywords C.I.=n and OPEN(n1,n2).

UHF The unrestricted Hartree-Fock Hamiltonian is to be used.

VECTors The eigenvectors are to be printed. In UHF calculations

both alpha and beta eigenvectors are printed; in all cases

the full set, occupied and virtual, are output. The

eigenvectors are normalized to unity, that is the sum of

the squares of the coefficients is exactly one. If DEBUG

is specified, then ALL eigenvectors on every iteration of

every SCF calculation will be printed. This is useful in

a learning context, but would normally be very undesirable.

Top

Description of the Generalized Hybrid Orbital (GHO) method

and the GLNK Command

[GLNK atom-selection]

atom-selection: contains a list of atoms that are boundary atoms.

Restrictions: The current implementation of the method requires that

ALL boundary atoms are placed at the end of the QM residue, or at

the end of the QM atom list. It is also strongly advised to treat

the entire QM fragment as a single residue, without any GROUPping

of atoms. This is because the delocalized nature of molecular

orbitals does not allow for arbitrarily excluding a particular

fragment or orbitals from interacting with other parts of the system.

Description: In addition to the link atom approach, a generalized

hybrid orbital (GHO) approach for the treatment of the division across

a covalent bond between the QM and MM region. The method recognizes

a frontier atom, typically carbon which is the only atom that has

its parameters optimized at this time, both as a QM atom and an MM

atom. Thus, standard basis orbitals are assigned to this atom.

These atomic orbitals on the frontier atoms are transformed into a

set of equivalent hybrid orbitals (typically the frontier atom is

of sp3 hybridization type). One of the four hybrid orbitals, which

points directly to the direction of the neighboring QM atom, is

included in QM-SCF orbital optimizations, and is an active orbital.

The other three hybrid orbitals are not optimized. Thus, they are the

auxillary orbitals. Since hybridization (contributions from s and

p orbitals to the hybrid orbitals) is dependent on the local geometry,

change of bond angles will lead to bond polarization in the active

orbital. Also, since the active orbital is being optimized in the

SCF procedure, charge transfer between the frontier atom and the

QM fragment is allowed. Consequently, the GHO method provides a

convenient way for smooth transition of charge distribution from the

QM region into the MM region.

The charge density on the auxilary orbitals are determined by equally

distributing the MM partial charge on the frontier atom. Thus,

P(mu mu) = 1 - q(mm)/3. The neutral group convention adopted by

the CHARMM force field makes it possible not to alter, to add, or

to delete any MM charges. Furthermore, no extra degrees of freedom

is introduced in the GHO approach.

The GHO method based on Unrestricted HF theory (GHO-UHF) is implemented

at semiempirical level (AM1, PM3) in the quantum module. With this

extension, GHO boundary treatment can be used for open shell QM fragments

in combined QM/MM calculations.

For a GHO-UHF wavefunction, we have two sets of auxiliary hybrid

orbitals for alpha spin and beta spin electrons respectively.

The charge density assigned to each of these auxiliary hybrid orbitals

is 0.5(1.0-q(mm)/3.0), while q(mm) denotes the MM partial charge of the

GHO boundary atom. Similar to GHO-RHF, the hybridization basis

transformation is carried out between the density matrix and Fock matrix,

both for the alpha and the beta sets.

Analytical gradients and Mulliken population analysis are also implemented

for GHO-UHF.

Limitations: The present implementation allows up to 5 QM-boundary

atoms, which uses psuedo-atomic numbers 91-95. Thus, elements 91

through 95 can not be used in QM calculations.

Reference: Reference made to the following paper, which contains

a more thorough description and discussion of test cases, is appreciated.

Jiali Gao, Patricia Amara, Cristobal Alhambra, and Martin J. Field,

J. Phys. Chem. 102, 4714-4721 (1998). "A Generalized Hybrid Orbital

(GHO) Approach for the Treatment of Link-Atoms using Combined

QM/MM Potentials."

Description of the Generalized Hybrid Orbital (GHO) method

and the GLNK Command

[GLNK atom-selection]

atom-selection: contains a list of atoms that are boundary atoms.

Restrictions: The current implementation of the method requires that

ALL boundary atoms are placed at the end of the QM residue, or at

the end of the QM atom list. It is also strongly advised to treat

the entire QM fragment as a single residue, without any GROUPping

of atoms. This is because the delocalized nature of molecular

orbitals does not allow for arbitrarily excluding a particular

fragment or orbitals from interacting with other parts of the system.

Description: In addition to the link atom approach, a generalized

hybrid orbital (GHO) approach for the treatment of the division across

a covalent bond between the QM and MM region. The method recognizes

a frontier atom, typically carbon which is the only atom that has

its parameters optimized at this time, both as a QM atom and an MM

atom. Thus, standard basis orbitals are assigned to this atom.

These atomic orbitals on the frontier atoms are transformed into a

set of equivalent hybrid orbitals (typically the frontier atom is

of sp3 hybridization type). One of the four hybrid orbitals, which

points directly to the direction of the neighboring QM atom, is

included in QM-SCF orbital optimizations, and is an active orbital.

The other three hybrid orbitals are not optimized. Thus, they are the

auxillary orbitals. Since hybridization (contributions from s and

p orbitals to the hybrid orbitals) is dependent on the local geometry,

change of bond angles will lead to bond polarization in the active

orbital. Also, since the active orbital is being optimized in the

SCF procedure, charge transfer between the frontier atom and the

QM fragment is allowed. Consequently, the GHO method provides a

convenient way for smooth transition of charge distribution from the

QM region into the MM region.

The charge density on the auxilary orbitals are determined by equally

distributing the MM partial charge on the frontier atom. Thus,

P(mu mu) = 1 - q(mm)/3. The neutral group convention adopted by

the CHARMM force field makes it possible not to alter, to add, or

to delete any MM charges. Furthermore, no extra degrees of freedom

is introduced in the GHO approach.

The GHO method based on Unrestricted HF theory (GHO-UHF) is implemented

at semiempirical level (AM1, PM3) in the quantum module. With this

extension, GHO boundary treatment can be used for open shell QM fragments

in combined QM/MM calculations.

For a GHO-UHF wavefunction, we have two sets of auxiliary hybrid

orbitals for alpha spin and beta spin electrons respectively.

The charge density assigned to each of these auxiliary hybrid orbitals

is 0.5(1.0-q(mm)/3.0), while q(mm) denotes the MM partial charge of the

GHO boundary atom. Similar to GHO-RHF, the hybridization basis

transformation is carried out between the density matrix and Fock matrix,

both for the alpha and the beta sets.

Analytical gradients and Mulliken population analysis are also implemented

for GHO-UHF.

Limitations: The present implementation allows up to 5 QM-boundary

atoms, which uses psuedo-atomic numbers 91-95. Thus, elements 91

through 95 can not be used in QM calculations.

Reference: Reference made to the following paper, which contains

a more thorough description and discussion of test cases, is appreciated.

Jiali Gao, Patricia Amara, Cristobal Alhambra, and Martin J. Field,

J. Phys. Chem. 102, 4714-4721 (1998). "A Generalized Hybrid Orbital

(GHO) Approach for the Treatment of Link-Atoms using Combined

QM/MM Potentials."

Top

Description of the DECO Command

[DECO]

The lone command DECO initiates an qm/mm interaction energy

decomposition calculation on the fly during a molecular dynamics simulation

using the QUANtum command. It is currently implemented only for

semiempirical Hamiltonians. The analysis is based on the method reported

in J. Gao and X. Xia, Science, 258, 631 (1992). It decomposes the total

QM/MM electrostatic interaction energy into a vertical interaction energy

Evert, and a polarization term Epol. The latter is further separated into

electrostatic stabilization Estab, and charge distortion Edist. These

terms are defined as follows (Y is the wave function of the qm system

in the presence of mm charges, and Yo is the wave function of the qm

system in the absence of mm charges, i.e., in the gas phase):

Eqm/mm = <Y|Hqm+Hqmmm(elec)|Y>

= Evert + Epol

Evert = <Yo|Hqmmm(elec)|Yo>

Epol = Eqm/mm - Evert

Epol = Estab + Edist

Estab = <Y|Hqmmm(elec)|Y> - <Yo|Hqmmm(elec)|Yo>

Edsit = <Y|Hqm|Y> - <Yo|Hqm|Yo>

where Hqm is the Hamiltonian of the qm system, and Hqmmm(elec) is

the electrostatic part of the QM/MM interaction Hamiltonian. Note that

the van der Waals term is kept track of separately within CHARMM's

general energy terms. In addition, the decomposition also averages

the average "gas-phase" energy <Egas> of the QM system during the QM/MM

simulation. Egas, of course, is NOT the true average gas-phase energy,

but it is one that is restrained by the presence of the MM field.

It is, however, interesting to note that <Egas> - <Yo|Hqm|Yo> gives

the "strain energy" due to geometrical strain in the condensed

phase/protein environment. JG 12/00

Description of the DECO Command

[DECO]

The lone command DECO initiates an qm/mm interaction energy

decomposition calculation on the fly during a molecular dynamics simulation

using the QUANtum command. It is currently implemented only for

semiempirical Hamiltonians. The analysis is based on the method reported

in J. Gao and X. Xia, Science, 258, 631 (1992). It decomposes the total

QM/MM electrostatic interaction energy into a vertical interaction energy

Evert, and a polarization term Epol. The latter is further separated into

electrostatic stabilization Estab, and charge distortion Edist. These

terms are defined as follows (Y is the wave function of the qm system

in the presence of mm charges, and Yo is the wave function of the qm

system in the absence of mm charges, i.e., in the gas phase):

Eqm/mm = <Y|Hqm+Hqmmm(elec)|Y>

= Evert + Epol

Evert = <Yo|Hqmmm(elec)|Yo>

Epol = Eqm/mm - Evert

Epol = Estab + Edist

Estab = <Y|Hqmmm(elec)|Y> - <Yo|Hqmmm(elec)|Yo>

Edsit = <Y|Hqm|Y> - <Yo|Hqm|Yo>

where Hqm is the Hamiltonian of the qm system, and Hqmmm(elec) is

the electrostatic part of the QM/MM interaction Hamiltonian. Note that

the van der Waals term is kept track of separately within CHARMM's

general energy terms. In addition, the decomposition also averages

the average "gas-phase" energy <Egas> of the QM system during the QM/MM

simulation. Egas, of course, is NOT the true average gas-phase energy,

but it is one that is restrained by the presence of the MM field.

It is, however, interesting to note that <Egas> - <Yo|Hqm|Yo> gives

the "strain energy" due to geometrical strain in the condensed

phase/protein environment. JG 12/00

Top

[ DAMP real ]

A simple density damping option is added to the SCF driver for the quantum

module. The motivation of adding this option is to provide a possibility to

overcome SCF convergence difficulties. Currently, this damping accelerator is

only used to limit oscillation behavior in GHO-UHF type calculations.

For an SCF iteration with density damping turned on, the actual density matrix

used for next iteration is computed by a linear combination of the current

density with the previous one:

P = a x P + (1-a) x P

i i-1 i

The damping factor "a" is a user defined floating point number between 0 and 1.

One can specify this damping factor as "DAMP a" in the QUANtum command line.

The default of this damping factor is 0.0, i.e., no damping at all. Any

damping factor being less than 0 or greater than 1 will incur a level -5

warning.

In the current implementation, several "damped" steps (with a user defined

damping factor "a" ) are carried out until the alpha and beta density matrices

are partially converged (density changes are smaller than 100 times the density

convergence criterion), then "undamped" steps (a=0.0) follow until the final

convergence is reached.

[ DAMP real ]

A simple density damping option is added to the SCF driver for the quantum

module. The motivation of adding this option is to provide a possibility to

overcome SCF convergence difficulties. Currently, this damping accelerator is

only used to limit oscillation behavior in GHO-UHF type calculations.

For an SCF iteration with density damping turned on, the actual density matrix

used for next iteration is computed by a linear combination of the current

density with the previous one:

P = a x P + (1-a) x P

i i-1 i

The damping factor "a" is a user defined floating point number between 0 and 1.

One can specify this damping factor as "DAMP a" in the QUANtum command line.

The default of this damping factor is 0.0, i.e., no damping at all. Any

damping factor being less than 0 or greater than 1 will incur a level -5

warning.

In the current implementation, several "damped" steps (with a user defined

damping factor "a" ) are carried out until the alpha and beta density matrices

are partially converged (density changes are smaller than 100 times the density

convergence criterion), then "undamped" steps (a=0.0) follow until the final

convergence is reached.

Top

Description of the PERT Command

[PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT]

REF0 lambda0 the reference Lambda value in a FEP calculation

PER1 lambda1 the forward perturbation Lambda value in a FEP calculation

PER2 lambda2 the reverse perturbation Lambda value in a FEP calculation

TEMP finalT the target or final temperature of the MD simulation

NOTE: this is required. Otherwise an error will occur.

The PERT command performs electrostatic free energy decoupling

calculation for QM/MM interactions on the fly of a molecular dynamics

simulation. The algorithm is based on a method described in J. Gao,

J. Phys. Chem. 96, 537 (1992). Through a series of simulations, the

electrostatic component of the free energy of solvation can be determined.

See, other free energy simulation documents.

Delta G(L0->L1) = -RT < exp(-[E{H(L1)}-E{H(L0)}]/RT > _E{H(L0)}

where

E{H(Li)} = <Y|Hqm + Li * Hqmmm(elec) + Hqmmm(vdW)|Y>

JG 12/00

Description of the PERT Command

[PERT REF0 lambda0 PER1 lambda1 PER2 lambda2 TEMP finalT]

REF0 lambda0 the reference Lambda value in a FEP calculation

PER1 lambda1 the forward perturbation Lambda value in a FEP calculation

PER2 lambda2 the reverse perturbation Lambda value in a FEP calculation

TEMP finalT the target or final temperature of the MD simulation

NOTE: this is required. Otherwise an error will occur.

The PERT command performs electrostatic free energy decoupling

calculation for QM/MM interactions on the fly of a molecular dynamics

simulation. The algorithm is based on a method described in J. Gao,

J. Phys. Chem. 96, 537 (1992). Through a series of simulations, the

electrostatic component of the free energy of solvation can be determined.

See, other free energy simulation documents.

Delta G(L0->L1) = -RT < exp(-[E{H(L1)}-E{H(L0)}]/RT > _E{H(L0)}

where

E{H(Li)} = <Y|Hqm + Li * Hqmmm(elec) + Hqmmm(vdW)|Y>

JG 12/00

Top

Simple Periodic Boundary Conditions for QM/MM calculations

This code is an extension of the algorithm already implemented in

duplication of coordinates to save memory in QM/MM calculations. It takes

advantage of the minimum image convention for a periodic cubic (or rectangular

or any other shapes) box such that crystallographic images are not required to

be generated in the psf (» images ).

[Syntax]

BOUNd {CUBOUNdary } {BOXL <real> } CUTNB <real>

CUBOUN = CUbicBOUNd

BOXL = length of the box edge

CUTNB = cutoff for generating "virtual" images

Note: QM/MM PBOUND is INCOMPATIBLE with atom based non-bonded list.

RESTRICTIONS:

1. Information about the periodic boundary must be given

to the program through the command READ IMAGE (» image )

2. The system must be centered using commands:

a) IMAGE (» image ) when solute and solvent

are small molecules (3-5 atoms)

b) CENT keyword in DYNA command line (» dynamc ) when solute is

a protein or large organic molecule.

3. The mm and qm/mm nonbonded lists (electrostatic and Van der Waals

interactions)

must be generated by groups, i.e:

update group fswitch vdw vswitched vgroup ...

4. Compile with PBOUND in pref.dat

Example:

...

! Set-up image information for cubic periodic boundaries

! cubig.img file in the /test/data/ directory

set 6 58.93044

set 7 58.93044

set 8 58.93044

open unit 1 read form name cubic.img

read image card unit 1

close unit 1

IMAGe byseg xcen 0.0 ycen 0.0 zcen 0.0 select segid prot end

IMAGe byres xcen 0.0 ycen 0.0 zcen 0.0 select sol end

BOUNd CUBOUND BOXL 58.93044 CUTNB 12.0

UPDAte group fswitch noextend cdie vdw vswitched eps 1.0 -

cutnb 12.0 ctofnb 11.5 ctonnb 10.5 vgroup WMIN 1.2 -

inbf 25 imgfrq 1000 cutim 12.0

QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 -

scfc 0.000001

DYNAmics vverlet rest nstep 15000 timestp 0.001 -

ilbfrq 0 iseed 324239 firstt 239.0 finalt 298.15 -

teminc 5.0 ihtfrq 5.0 iasor 0 iasvel 1 iscvel 0 -

ichecw 1 ieqfrq 200 nprint 100 nsavc 00 -

nose tref 298.15 qref 50.0 isvfrq 100 -

tstruc 298.15 -

twindh 5 twindl -5 iprfrq 2000 wmin 0.9 -

iunrea 9 iunwri 10 iuncrd 11 iunvel -1 kunit -12 -

CENT ncres 162

....

Simple Periodic Boundary Conditions for QM/MM calculations

This code is an extension of the algorithm already implemented in

duplication of coordinates to save memory in QM/MM calculations. It takes

advantage of the minimum image convention for a periodic cubic (or rectangular

or any other shapes) box such that crystallographic images are not required to

be generated in the psf (» images ).

[Syntax]

BOUNd {CUBOUNdary } {BOXL <real> } CUTNB <real>

CUBOUN = CUbicBOUNd

BOXL = length of the box edge

CUTNB = cutoff for generating "virtual" images

Note: QM/MM PBOUND is INCOMPATIBLE with atom based non-bonded list.

RESTRICTIONS:

1. Information about the periodic boundary must be given

to the program through the command READ IMAGE (» image )

2. The system must be centered using commands:

a) IMAGE (» image ) when solute and solvent

are small molecules (3-5 atoms)

b) CENT keyword in DYNA command line (» dynamc ) when solute is

a protein or large organic molecule.

3. The mm and qm/mm nonbonded lists (electrostatic and Van der Waals

interactions)

must be generated by groups, i.e:

update group fswitch vdw vswitched vgroup ...

4. Compile with PBOUND in pref.dat

Example:

...

! Set-up image information for cubic periodic boundaries

! cubig.img file in the /test/data/ directory

set 6 58.93044

set 7 58.93044

set 8 58.93044

open unit 1 read form name cubic.img

read image card unit 1

close unit 1

IMAGe byseg xcen 0.0 ycen 0.0 zcen 0.0 select segid prot end

IMAGe byres xcen 0.0 ycen 0.0 zcen 0.0 select sol end

BOUNd CUBOUND BOXL 58.93044 CUTNB 12.0

UPDAte group fswitch noextend cdie vdw vswitched eps 1.0 -

cutnb 12.0 ctofnb 11.5 ctonnb 10.5 vgroup WMIN 1.2 -

inbf 25 imgfrq 1000 cutim 12.0

QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 -

scfc 0.000001

DYNAmics vverlet rest nstep 15000 timestp 0.001 -

ilbfrq 0 iseed 324239 firstt 239.0 finalt 298.15 -

teminc 5.0 ihtfrq 5.0 iasor 0 iasvel 1 iscvel 0 -

ichecw 1 ieqfrq 200 nprint 100 nsavc 00 -

nose tref 298.15 qref 50.0 isvfrq 100 -

tstruc 298.15 -

twindh 5 twindl -5 iprfrq 2000 wmin 0.9 -

iunrea 9 iunwri 10 iuncrd 11 iunvel -1 kunit -12 -

CENT ncres 162

....

Top

Description of the GROUp keyword

[ GROUp]

The QM/MM module that was initially implemented into CHARMM allows

for separate QM group and MM group interactions, where a "QM" molecule

can be divided into several groups. The GROUp option allows the QM

molecule to be partitioned into separate groups for generating non-bonded

list, but keeps the interactions between the ENTIRE QM molecule and any

MM group that is whithin the cutoff of any one qm group, avoiding the

possibility that some MM group only interact with part of the QM molecule.

This is necessary because the QM molecule is not divisible as the wave

function is delocalized over the entire molecule. (June, 2001)

See also description of the GLNK keyword.

Description of the GROUp keyword

[ GROUp]

The QM/MM module that was initially implemented into CHARMM allows

for separate QM group and MM group interactions, where a "QM" molecule

can be divided into several groups. The GROUp option allows the QM

molecule to be partitioned into separate groups for generating non-bonded

list, but keeps the interactions between the ENTIRE QM molecule and any

MM group that is whithin the cutoff of any one qm group, avoiding the

possibility that some MM group only interact with part of the QM molecule.

This is necessary because the QM molecule is not divisible as the wave

function is delocalized over the entire molecule. (June, 2001)

See also description of the GLNK keyword.

Top

Description of the CHDYn keyword

[CHDYn]

CHDYn allows the computation of average Mulliken population charges

on quantum atoms during a molecular dynamics simulation. It prints the

averaged atomic charges at every IPRFRQ steps.

When CHDYn is used along with DECO it will result in the calculation

of average atomic charges for the same trajectory in the presence of

the MM bath (condensed phase) and absence of the MM charges (gas phase).

RESTRICTIONS: CHDYn is only implemented for molecular dynamics calculations

with the Leapfrog Verlet and Velocity Verlet integrators.

TESTCASE : qmfep.inp

Description of the CHDYn keyword

[CHDYn]

CHDYn allows the computation of average Mulliken population charges

on quantum atoms during a molecular dynamics simulation. It prints the

averaged atomic charges at every IPRFRQ steps.

When CHDYn is used along with DECO it will result in the calculation

of average atomic charges for the same trajectory in the presence of

the MM bath (condensed phase) and absence of the MM charges (gas phase).

RESTRICTIONS: CHDYn is only implemented for molecular dynamics calculations

with the Leapfrog Verlet and Velocity Verlet integrators.

TESTCASE : qmfep.inp

Top

Description of the NEWDS Command

[ NEWD int ] ewald-spec

ewald-spec::= { [ KMAX integer ] } KSQMAX integer

{ KMXX integer KMXY integer KMXZ integer }

A simple Ewald sum method is implemented into the QM/MM potential. A full

description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2.

This is based on regular Ewald sum method and share similar keywords

(» ewald ).

The defaults for the QM/MM-Ewald calculations are set internally

and are currently set to NEWD 1, KMAX=5, KSQMax=27, where the

KMAX keyword is the number of kvectors (or images of the

primary unit cell) that will be summed in any direction. It is the

radius of the Ewald summation. For orthorombic cells, the value of

kmax may be independently specified in the x, y, and z directions with

the keywords KMXX, KMXY, and KMXZ. But, different from regular Ewald in

in MM part.

The KSQMax key word should be chosen between KMAX squared and 3 times

KMAX squared, and KAPPA value share the exact same number you use in Nonbond

options.

Specific for SQUANTM: implementation of QM/MM-PME method.

PME version fo QM/MM-Ewald summation is the default for SQUANTM module. (You

can use regualr QM/MM-Ewald method by adding a keyword NOPMEwald.) Whenever

MM-MM long-range electrostatic interactions are computed by using PME method,

QM-MM interactions in the QM/MM-Ewald are also computed by PME method, where

the potential at the QM atom sites are computed by PME algorithm. The

gradients component by QM-MM interactions at the QM and MM atom sites are

also computed by PME algorithm, which is separatedly calculated from the

MM-MM PME contributions. Still, the long-range QM-QM interactions are

computed by a regular QM/MM-Ewald method, this requires users to specify

the ewald-spec options, otherwise defauls values will be invoked. The

QM/MM-PME method is much faster and requires less memory.

Description of the NEWDS Command

[ NEWD int ] ewald-spec

ewald-spec::= { [ KMAX integer ] } KSQMAX integer

{ KMXX integer KMXY integer KMXZ integer }

A simple Ewald sum method is implemented into the QM/MM potential. A full

description of theory is described in J. Chem. Theory. Comput. (2005) 1, 2.

This is based on regular Ewald sum method and share similar keywords

(» ewald ).

The defaults for the QM/MM-Ewald calculations are set internally

and are currently set to NEWD 1, KMAX=5, KSQMax=27, where the

KMAX keyword is the number of kvectors (or images of the

primary unit cell) that will be summed in any direction. It is the

radius of the Ewald summation. For orthorombic cells, the value of

kmax may be independently specified in the x, y, and z directions with

the keywords KMXX, KMXY, and KMXZ. But, different from regular Ewald in

in MM part.

The KSQMax key word should be chosen between KMAX squared and 3 times

KMAX squared, and KAPPA value share the exact same number you use in Nonbond

options.

Specific for SQUANTM: implementation of QM/MM-PME method.

PME version fo QM/MM-Ewald summation is the default for SQUANTM module. (You

can use regualr QM/MM-Ewald method by adding a keyword NOPMEwald.) Whenever

MM-MM long-range electrostatic interactions are computed by using PME method,

QM-MM interactions in the QM/MM-Ewald are also computed by PME method, where

the potential at the QM atom sites are computed by PME algorithm. The

gradients component by QM-MM interactions at the QM and MM atom sites are

also computed by PME algorithm, which is separatedly calculated from the

MM-MM PME contributions. Still, the long-range QM-QM interactions are

computed by a regular QM/MM-Ewald method, this requires users to specify

the ewald-spec options, otherwise defauls values will be invoked. The

QM/MM-PME method is much faster and requires less memory.

Top

[EXTErnal PUNIt int]

EXTE Allows reading the semi-empirical parameters from an external file.

The format is as follows (free format):

PARNAME1 ATOMTYPE1 PARVALUE1

PARNAME2 ATOMTYPE2 PARVALUE2

...

END

Empty lines are ignored

Acceptable parameters names are:

ALFA(ALP),BETAS,BETAP,BETAD,ZS,ZP,ZD,USS,UPP,UDD,GSS,GPP,GSP,GP2,HSP,

VS,VP,K1(FN11),L1(FN21),M1(FN31),K2(FN12),L2(FN22),M2(FN32),K3(FN13),

L3(FN23),M3(FN33),K4(FN14),L4(FN24),M4(FN34)

The following derived parameters are computed automatically:

EISOL,DD,QQ,AM,AD,AQ

Example:

USS H -11.3336021333

BETAS H -6.1735981344

END

[EXTErnal PUNIt int]

EXTE Allows reading the semi-empirical parameters from an external file.

The format is as follows (free format):

PARNAME1 ATOMTYPE1 PARVALUE1

PARNAME2 ATOMTYPE2 PARVALUE2

...

END

Empty lines are ignored

Acceptable parameters names are:

ALFA(ALP),BETAS,BETAP,BETAD,ZS,ZP,ZD,USS,UPP,UDD,GSS,GPP,GSP,GP2,HSP,

VS,VP,K1(FN11),L1(FN21),M1(FN31),K2(FN12),L2(FN22),M2(FN32),K3(FN13),

L3(FN23),M3(FN33),K4(FN14),L4(FN24),M4(FN34)

The following derived parameters are computed automatically:

EISOL,DD,QQ,AM,AD,AQ

Example:

USS H -11.3336021333

BETAS H -6.1735981344

END

Top

Description of the LEPS Command

[LEPS LEPA int LEPB int LEPC int -

D1AB real D1BC real D1AC real -

R1AB real R1BC real R1AC reat -

B1AB real B1BC real B1AC real -

S1AB real S1BC real S1AC real -

D2AB real D2BC real D2AC real -

R2AB real R2BC real R2AC real -

B2AB real B2BC real B2AC real -

S2AB real S2BC real S2AC real]

Description: The motivation behind the semiempirical valence bond term (SEVB)

is to improve the quality of the potential energy surface (PES) when using

semiempirical hamiltonians (AM1 or PM3) to model the reactive event in

enzyme active sites. NDDO based hamiltonias represent a cheap alternative

to describe reactions in enzyme active sites. They allow for a quantum

mechanical description of the active site together with an extensive sampling

of the protein configurational space when combined qmm/mm techniques are used.

However the savings in computer time come with sacrifices in the quality of

the PES due to the NDDO approximation. The SEVB term is introduced in the

hamiltonian of the system to palliate this problem. It contains two extended

London-Eiring-Polany-Sato (LEPS) equations for the three body subsystem

{A,B,C}. This reduced subsystem mimics the transfer of the particle B

between centers A and C in the active site. In most of the applications

B is a light atom like hydrogen and A and C correspond to the donor and

acceptor sites,

A-B + C ---> A + B-C

Each of the two extended LEPS functions have different parameters and depend

on the distances r(A-B), r(B-C), and r(A-C). One LEPS potential (V(ref))is

fitted to reproduce high ab initio or experimental data for a model reaction

whilst the second one (V(NDDO)) is fitted to the NDDO hamiltonian in use.

Finally the SEVB correction is introduced in the hamiltonian of the system

as the difference V(ref)-V(NDDO).

Syntaxis: The keyword LEPS in the command line QUANtum turns on the

routine that evaluates the SEVB correction. The three atoms needed to

evaluate the distances r(A-B), r(B-C), and r(A-C) are indicated by,

LEPA - donor center.

LEPB - transferred atom.

LEPC - acceptor center.

int - corresponds to the psf number of the respective atom.

The value of the parameters to build the functions V(NDDO) and V(ref) are,

. for the NDDO LEPS functions,

D1AB - dissociation energy for the diatomic A-B

D1BC - dissociation energy for the diatomic B-C

D1AC - dissociation energy for the diatomic A-C

R1AB - equilibrium distance for the diatomic A-B

R1BC - equilibrium distance for the diatomic B-C

R1AC - equilibrium distance for the diatomic A-C

B1AB - beta exponent for the diatomic A-B

B1BC - beta exponent for the diatomic B-C

B1AC - beta exponent for the diatomic A-C

S1AB - Sato parameter for the diatomic A-B

S1BC - Sato parameter for the diatomic B-C

S1AC - Sato parameter for the diatomic A-C

. for the reference LEPS functions,

D2AB - dissociation energy for the diatomic A-B

D2BC - dissociation energy for the diatomic B-C

D2AC - dissociation energy for the diatomic A-C

R2AB - equilibrium distance for the diatomic A-B

R2BC - equilibrium distance for the diatomic B-C

R2AC - equilibrium distance for the diatomic A-C

B2AB - beta exponent for the diatomic A-B

B2BC - beta exponent for the diatomic B-C

B2AC - beta exponent for the diatomic A-C

S2AB - Sato parameter for the diatomic A-B

S2BC - Sato parameter for the diatomic B-C

S2AC - Sato parameter for the diatomic A-C

A real value is expected after each one of them.

Limitations: The current implementation is only intended for a single SEVB

correcting term.

Reference: A detailed description of the LEPS potential energy functionals

as well as the application to an enzymatic hydride transfer can be found in,

C. Alhambra, J. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao &

D. G. Truhlar, Journal of Physical Chemistry B, 2001, 105, 11326-11340.

"Canonical Variational Theory for Enzyme Kinetics with the Protein Mean

Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory

and Application to Liver Alcohol Dehydrogenase."

Description of the LEPS Command

[LEPS LEPA int LEPB int LEPC int -

D1AB real D1BC real D1AC real -

R1AB real R1BC real R1AC reat -

B1AB real B1BC real B1AC real -

S1AB real S1BC real S1AC real -

D2AB real D2BC real D2AC real -

R2AB real R2BC real R2AC real -

B2AB real B2BC real B2AC real -

S2AB real S2BC real S2AC real]

Description: The motivation behind the semiempirical valence bond term (SEVB)

is to improve the quality of the potential energy surface (PES) when using

semiempirical hamiltonians (AM1 or PM3) to model the reactive event in

enzyme active sites. NDDO based hamiltonias represent a cheap alternative

to describe reactions in enzyme active sites. They allow for a quantum

mechanical description of the active site together with an extensive sampling

of the protein configurational space when combined qmm/mm techniques are used.

However the savings in computer time come with sacrifices in the quality of

the PES due to the NDDO approximation. The SEVB term is introduced in the

hamiltonian of the system to palliate this problem. It contains two extended

London-Eiring-Polany-Sato (LEPS) equations for the three body subsystem

{A,B,C}. This reduced subsystem mimics the transfer of the particle B

between centers A and C in the active site. In most of the applications

B is a light atom like hydrogen and A and C correspond to the donor and

acceptor sites,

A-B + C ---> A + B-C

Each of the two extended LEPS functions have different parameters and depend

on the distances r(A-B), r(B-C), and r(A-C). One LEPS potential (V(ref))is

fitted to reproduce high ab initio or experimental data for a model reaction

whilst the second one (V(NDDO)) is fitted to the NDDO hamiltonian in use.

Finally the SEVB correction is introduced in the hamiltonian of the system

as the difference V(ref)-V(NDDO).

Syntaxis: The keyword LEPS in the command line QUANtum turns on the

routine that evaluates the SEVB correction. The three atoms needed to

evaluate the distances r(A-B), r(B-C), and r(A-C) are indicated by,

LEPA - donor center.

LEPB - transferred atom.

LEPC - acceptor center.

int - corresponds to the psf number of the respective atom.

The value of the parameters to build the functions V(NDDO) and V(ref) are,

. for the NDDO LEPS functions,

D1AB - dissociation energy for the diatomic A-B

D1BC - dissociation energy for the diatomic B-C

D1AC - dissociation energy for the diatomic A-C

R1AB - equilibrium distance for the diatomic A-B

R1BC - equilibrium distance for the diatomic B-C

R1AC - equilibrium distance for the diatomic A-C

B1AB - beta exponent for the diatomic A-B

B1BC - beta exponent for the diatomic B-C

B1AC - beta exponent for the diatomic A-C

S1AB - Sato parameter for the diatomic A-B

S1BC - Sato parameter for the diatomic B-C

S1AC - Sato parameter for the diatomic A-C

. for the reference LEPS functions,

D2AB - dissociation energy for the diatomic A-B

D2BC - dissociation energy for the diatomic B-C

D2AC - dissociation energy for the diatomic A-C

R2AB - equilibrium distance for the diatomic A-B

R2BC - equilibrium distance for the diatomic B-C

R2AC - equilibrium distance for the diatomic A-C

B2AB - beta exponent for the diatomic A-B

B2BC - beta exponent for the diatomic B-C

B2AC - beta exponent for the diatomic A-C

S2AB - Sato parameter for the diatomic A-B

S2BC - Sato parameter for the diatomic B-C

S2AC - Sato parameter for the diatomic A-C

A real value is expected after each one of them.

Limitations: The current implementation is only intended for a single SEVB

correcting term.

Reference: A detailed description of the LEPS potential energy functionals

as well as the application to an enzymatic hydride transfer can be found in,

C. Alhambra, J. Corchado, M. L. Sanchez, M. Garcia-Viloca, J. Gao &

D. G. Truhlar, Journal of Physical Chemistry B, 2001, 105, 11326-11340.

"Canonical Variational Theory for Enzyme Kinetics with the Protein Mean

Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory

and Application to Liver Alcohol Dehydrogenase."

Top

Description of SVB command

[ LEPS SVB LEPA int LEPB int LEPC int -

D1AB real D1BC real D1AC real -

R1AB real R1BC real R1AC reat -

B1AB real B1BC real B1AC real ]

Description: A simple analytical function is included in combined QM/MM

potential energy functions using semiempirical Hamiltonian for enzyme

reactions to obtain more accurate energetic results. The motivation

behind the simple valence bond (SVB) term is to introduce small energy

corrections at critical points (reactants, transition state, and products)

on the QM potential energy surface. The underlying assumption is that the

general shape of the QM potential energy surface at the semiempirical level

is in reasonable accord with high-level ab initio result. The SVB term

is a simplified version of the semiempirical valence bond term (SEVB)

invoked by the command LEPS.

The SVB term is a combination of two Morse potentials, which depend on

the bond distances of the breaking and making bonds, respectively, and

a coupling term that is typically (but not exclusively) a function of

the donor-acceptor distance.

Specifically, for the reaction A-B + C ---> A + B-C

with r1 = distance A-B

r2 = distance B-C

r3 = distance A-C

the SVB correction along a given reaction coordinate that depends on r1 and r2

is:

VSVB = 1/2 [ M1(r1)+M2(r2) - [(M2(r2)-M1(r1))**2+4V12**2)]**1/2]

where M1(r1) and M2(r2) are Morse potentials:

M1(r1) = D1AB [ exp(-2*B1AB*(r1-R1AB))-2*exp(-B1AB*(r1-R1AB)) ]

M2(r2) = D1BC [ exp(-2*B1BC*(r2-R1BC))-2*exp(-B1BC*(r1-R1BC)) ]

and the coupling term has the form:

V12 = D1AC * exp(-B1AC*(r3-R1AC))

where,

D1AB = difference in dissociation energy between the reference calculation

or experimental value and the dissociation energy given by

semiempirical method (for the AB bond)

D1BC = difference in dissociation energy between reference calculation

or experimental value and the dissociation energy given by

the semiempirical method (for the BC bond)

B1AB and B1BC = related to the bond force constants (kij)

and to the bond dissociation energies (D1ij) by

B1ij = sqrt (kij/2*D1ij). These values can be obtained from

experimentally determined frequencies or from high level

calculations.

R1AB, R1BC and R1AC = equilibrium bond length for bonds AB, BC, and AC,

respectively.

D1AC,R1AC = adjustable parameters to obtain the desired barrier height.

Note: D1AB and D1BC may be also adjusted to obtain the desired reaction energy.

The difference D1AB-D1BC is the relative correction of the product state energy

respect to the reactant state energy. It is recommended to avoid negative values

for these variables.

Reference: A detailed description of the SVB method

as well as the application to the nucleophilic addition reaction catalized by

haloalkane dehalogenase is found in:

Devi-Kesavan, L.S.; Garcia-Viloca, M.; Gao, J. Theor.Chem.Acc. 2002, in press.

Example:

...

QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 -

scfc 0.000001 -

LEPS SVB LEPA 57 LEPB 58 LEPC 13 - ! atoms involved

D1AB 36.0 D1BC 15.0 D1AC 15.0 - ! energies

R1AB 1.101 R1BC 1.1011 R1AC 2.707 - ! equil. bond lenghts

B1AB 1.393 B1BC 1.409 B1AC 1.0 - ! exponents

...

File: qmmm, Node: 2DSVB, Up: Top, Previous: SVB, Next: SQUANTUM

The following options allow one to construct a two-dimensional simple

VB-like function to correct the (presumably) semiempirical QM/MM

potential energy surface. This extends beyong the one-dimensional

correction described above.

[LEPS

[LEPA int LEPB int LEPC int

D1AB real D1BC real D1AC real

R1AB real R1BC real R1AC real

B1AB real B1BC real B1AC real

S1AB real S1BC real S1AC real

D2AB real D2BC real D2AC real

R2AB real R2BC real R2AC real

B2AB real B2BC real B2AC real

S2AB real S2BC real S2AC real]

[SVB [SURF] [TEST] [GCOU|G1CO|G2CO]

LEPA int LEPB int [LEPC int]

D1AB real D1BC real [D1AC real]

R1AB real R1BC real [R1AC real]

B1AB real B1BC real [B1AC real]

[LEPD int LEPE int [LEPF int]

D1DE real D1EF real [D1DF real]

R1DE real R1EF real [R1DF real]

B1DE real B1EF real [B1DF real]

[VC12]]]

SVB SVB turns on the Simple Valence Bond correction function.

It requires correction values as difference between experimental

or high-level QM level data and the semi-empirical level used.

The following keywords work only with the SVB option.

SURFace A two-dimensional correction term is employed

TEST Additional output regarding SVB term at each energy step. Useful

when testing the extent of correction needed.

GCOUpling Use a gaussian coupling term which is a function of the reaction

coordinate. If SURF is also switched on, this keyword will switch

on gaussian terms for both coordinates.

G1COuple Use gaussian coupling term for first coordinate.

G2COuple Use gaussian coupling term for second coordinate.

VC12 Add coupling term between two coordinates. This term is currently

only a constant number.

If only two atoms are specified (LEPA and LEPB or LEPD and LEPE), a simple

exponential term between the two atoms will be added. If a gaussian term

is switched on via the GCOU,G1CO, or G2CO keywords, then a gaussian term

will be employed instead.

Description of SVB command

[ LEPS SVB LEPA int LEPB int LEPC int -

D1AB real D1BC real D1AC real -

R1AB real R1BC real R1AC reat -

B1AB real B1BC real B1AC real ]

Description: A simple analytical function is included in combined QM/MM

potential energy functions using semiempirical Hamiltonian for enzyme

reactions to obtain more accurate energetic results. The motivation

behind the simple valence bond (SVB) term is to introduce small energy

corrections at critical points (reactants, transition state, and products)

on the QM potential energy surface. The underlying assumption is that the

general shape of the QM potential energy surface at the semiempirical level

is in reasonable accord with high-level ab initio result. The SVB term

is a simplified version of the semiempirical valence bond term (SEVB)

invoked by the command LEPS.

The SVB term is a combination of two Morse potentials, which depend on

the bond distances of the breaking and making bonds, respectively, and

a coupling term that is typically (but not exclusively) a function of

the donor-acceptor distance.

Specifically, for the reaction A-B + C ---> A + B-C

with r1 = distance A-B

r2 = distance B-C

r3 = distance A-C

the SVB correction along a given reaction coordinate that depends on r1 and r2

is:

VSVB = 1/2 [ M1(r1)+M2(r2) - [(M2(r2)-M1(r1))**2+4V12**2)]**1/2]

where M1(r1) and M2(r2) are Morse potentials:

M1(r1) = D1AB [ exp(-2*B1AB*(r1-R1AB))-2*exp(-B1AB*(r1-R1AB)) ]

M2(r2) = D1BC [ exp(-2*B1BC*(r2-R1BC))-2*exp(-B1BC*(r1-R1BC)) ]

and the coupling term has the form:

V12 = D1AC * exp(-B1AC*(r3-R1AC))

where,

D1AB = difference in dissociation energy between the reference calculation

or experimental value and the dissociation energy given by

semiempirical method (for the AB bond)

D1BC = difference in dissociation energy between reference calculation

or experimental value and the dissociation energy given by

the semiempirical method (for the BC bond)

B1AB and B1BC = related to the bond force constants (kij)

and to the bond dissociation energies (D1ij) by

B1ij = sqrt (kij/2*D1ij). These values can be obtained from

experimentally determined frequencies or from high level

calculations.

R1AB, R1BC and R1AC = equilibrium bond length for bonds AB, BC, and AC,

respectively.

D1AC,R1AC = adjustable parameters to obtain the desired barrier height.

Note: D1AB and D1BC may be also adjusted to obtain the desired reaction energy.

The difference D1AB-D1BC is the relative correction of the product state energy

respect to the reactant state energy. It is recommended to avoid negative values

for these variables.

Reference: A detailed description of the SVB method

as well as the application to the nucleophilic addition reaction catalized by

haloalkane dehalogenase is found in:

Devi-Kesavan, L.S.; Garcia-Viloca, M.; Gao, J. Theor.Chem.Acc. 2002, in press.

Example:

...

QUANtum group sele qms end glnk sele bynu 68:69 end am1 charge 1 -

scfc 0.000001 -

LEPS SVB LEPA 57 LEPB 58 LEPC 13 - ! atoms involved

D1AB 36.0 D1BC 15.0 D1AC 15.0 - ! energies

R1AB 1.101 R1BC 1.1011 R1AC 2.707 - ! equil. bond lenghts

B1AB 1.393 B1BC 1.409 B1AC 1.0 - ! exponents

...

File: qmmm, Node: 2DSVB, Up: Top, Previous: SVB, Next: SQUANTUM

The following options allow one to construct a two-dimensional simple

VB-like function to correct the (presumably) semiempirical QM/MM

potential energy surface. This extends beyong the one-dimensional

correction described above.

[LEPS

[LEPA int LEPB int LEPC int

D1AB real D1BC real D1AC real

R1AB real R1BC real R1AC real

B1AB real B1BC real B1AC real

S1AB real S1BC real S1AC real

D2AB real D2BC real D2AC real

R2AB real R2BC real R2AC real

B2AB real B2BC real B2AC real

S2AB real S2BC real S2AC real]

[SVB [SURF] [TEST] [GCOU|G1CO|G2CO]

LEPA int LEPB int [LEPC int]

D1AB real D1BC real [D1AC real]

R1AB real R1BC real [R1AC real]

B1AB real B1BC real [B1AC real]

[LEPD int LEPE int [LEPF int]

D1DE real D1EF real [D1DF real]

R1DE real R1EF real [R1DF real]

B1DE real B1EF real [B1DF real]

[VC12]]]

SVB SVB turns on the Simple Valence Bond correction function.

It requires correction values as difference between experimental

or high-level QM level data and the semi-empirical level used.

The following keywords work only with the SVB option.

SURFace A two-dimensional correction term is employed

TEST Additional output regarding SVB term at each energy step. Useful

when testing the extent of correction needed.

GCOUpling Use a gaussian coupling term which is a function of the reaction

coordinate. If SURF is also switched on, this keyword will switch

on gaussian terms for both coordinates.

G1COuple Use gaussian coupling term for first coordinate.

G2COuple Use gaussian coupling term for second coordinate.

VC12 Add coupling term between two coordinates. This term is currently

only a constant number.

If only two atoms are specified (LEPA and LEPB or LEPD and LEPE), a simple

exponential term between the two atoms will be added. If a gaussian term

is switched on via the GCOU,G1CO, or G2CO keywords, then a gaussian term

will be employed instead.

Top

**********************************************************************

****** SQUANTUM MODULE ******

Combined Quantum Mechanical and Molecular Mechanics Method

Based on SQUANTM in CHARMM

The F90 semiempirical code written by Ross Walker (TSRI, AMBER) and

Mike Crowley (TSRI, AMBER and CHARMM), the interface to CHARMM has

been implemented by Kwangho Nam (UMN, nam@chem.umn.edu) including

GHO and Swithing function implementation. The QM/MM-Ewald summation

implementation is done as a joint project between TSRI and

UMN (University of Minnesota).

The new semiempirical code, SQUANTM, is envisioned to eventually

replace the current semiempirical QM code, which was originally

incorporated into CHARMM by Martin Field and Paul Bash based on

Stewart's MOPAC version 5 program. The SQUANTM was written in

Fortran90, and the result is a substantial improvement in

computational speed. However, the two packages are not in conflict

as long as they are not compiled together. Therefore, all the

original MOPAC-based QM/MM options and commands are kept.

Should a user choose to use the SQUANTM or the MOPAC-based QM/MM

algorithm, one simply follow the compiling steps highlighted below.

**********************************************************************

****** SQUANTUM MODULE ******

Combined Quantum Mechanical and Molecular Mechanics Method

Based on SQUANTM in CHARMM

The F90 semiempirical code written by Ross Walker (TSRI, AMBER) and

Mike Crowley (TSRI, AMBER and CHARMM), the interface to CHARMM has

been implemented by Kwangho Nam (UMN, nam@chem.umn.edu) including

GHO and Swithing function implementation. The QM/MM-Ewald summation

implementation is done as a joint project between TSRI and

UMN (University of Minnesota).

The new semiempirical code, SQUANTM, is envisioned to eventually

replace the current semiempirical QM code, which was originally

incorporated into CHARMM by Martin Field and Paul Bash based on

Stewart's MOPAC version 5 program. The SQUANTM was written in

Fortran90, and the result is a substantial improvement in

computational speed. However, the two packages are not in conflict

as long as they are not compiled together. Therefore, all the

original MOPAC-based QM/MM options and commands are kept.

Should a user choose to use the SQUANTM or the MOPAC-based QM/MM

algorithm, one simply follow the compiling steps highlighted below.

Top

Syntax for SQUANTM commands

QUANtum [atom-selection] [GLNK atom-selection]

[REMOve] [SWITched]

[AM1|PM3|MNDO|PDP3|PDMN] [CHARge int] [NOGAussian] [NDIS]

[SCFCriteria real]

[DOUBLET|TRIPLET]

[NEWD int] ewald-spec NOPMEwald

[DUALqm] { [PERTurbation pert-spec] }

{ [MLAYered mlay-spec] }

ewald-spec::= { [KMAX int] } [KSQMAX int]

{ [KMXX int] [KMXY int] [KMXZ int] }

pert-spec ::= [atom-selection] [KHARge int] [GLN2 atom-selection]

[REF0 real] [PEF1 real] [PEF2 real]

[TEMP real]

[PKAP] { [NOMM] }

{ [NOAN] [NODI] [NOIM] }

mlay-spec ::= [atom-selection] [KHARge int] [LINK atom-selection]

[RCUT real]

(**mlay-spec: refer the comments below.)

GLNK: GHO method implementation (refer qmmm.info).

REMOve: Classical energies within QM atoms are removed.

SWITched: Use switching function from CTONNB to CTOFNB values

based on GROUp method (refer nbonds.info). It is

incompatible with NEWD options

AM1|PM3|MNDO|PDP3|PDMN: AM1 model, PM3 model, MNDO model,

PDDG/PM3 (PDP3) model, and PDDG/MNDO (PDMN) model.

Note: currently, GHO method only support AM1 and

PM3 model.

For PDDG/PM3 and PDDG/MNDO model, the reference

is Repasky et al. J. Comput. Chem. (2002), 23, 1601.

NOGAussian: This will turn off Gaussian core-core interaction

between QM and MM pairs in the AM1 and PM3 model.

As a default, the Gaussian core-core interactions

will be computed.

NDIS : Turn off DIIS converger. (default is .false.)

NEWD and ewald-spec: refer the description for QUANTUM module.

NOPMEwald: Use regualr QM/MM-Ewald summation methods. (Default is false.)

This is added for backward compatibility. Note that only for

SQUANTM supports QM/MM-PME (refer details for NEWD description.)

DUALqm : Use dual qm/mm calculations. (Multiple qm/mm region

or FEP calculation.)

PERTurbation and pert-spec : Do FEP pKa calculations.

The reactant state (lambda=0) should be

the protonated state, and the product state

should be the deprotonated state (lambda=1).

The perturbation is only applied to the

electrostatic interactions between QM and

MM pairs.

H_eff = (1-lambda)*H_reactant + (lambda)*H_product

atom-selection: atom selection for the product state (lambda=1).

Mostly, this atom selection lacks the H atom that is

annihilated in the FEP calculations.

KHARge : charge for 2nd qm region (product state).

GLN2 : use GHO method in the 2nd qm region.

REF0/PEF1/PEF2/TEMP : refer section for "Description of the PERT Command"

(above).

PKAP : turn on mm valency terms for pKa calculation, in particular,

for dummy H-atom.

In the product state, the H atom (for the protonated state)

is changed into mm dummy atom that is not interact with other

atoms (mm and qm atoms) electrostatically, while the bond,

angle, dihedral, and improper terms are maintained to avoid

the end point problem during the FEP calculations. (Refer the

approach of Riccardi et al. J. Phys. Chem. B (2005), 105,

17715.)

NOMM : turn off the angle/dihedral/improper terms for dummy H-atom.

NOAN / NODI / NOIM : specifically turn off either angle, dihedral, or

improper terms.

("NOMM" is same as "NOAN NODI NOIM.")

**Note that the bond terms are maintained.**

MLAYered and mlay-spec: Do multi-layered qm/mm calculations.

This is similar to the electronically embedded ONIOM

type potential. The 1st qm/mm layer has a larger qm

selection, and the 2nd qm/mm layer has a smaller qm

selection but is a subset of the 1st qm selection.

The total energy is extrapolated from the ab initio

and semiempirical qm/mm calculations. Therefore, it

assumes the potential at the semiempirical level for

the larger qm region is corrected at the ab initio

level for the smaller qm region, and the 2nd qm region

should be chosen with care.

E_tot = {E_semi-qm/mm (1st qm/mm region)}

+ {E_ai-qm/mm (2nd qm/mm region) - E_semi-qm/mm (2nd qm/mm region)}

**Note that only GAMESS-UK is tested with SQUANTM, and check for future

update for GAMESS-US. To compile for this, use both U and SQ in the

install.com.

atom-selection: atom selection for the 2nd qm region. (This should be a subset

of 1st qm selection.)

KHARge : charge for the 2nd qm region.

LINK atom-sele: selection for (2nd) qm atoms to which the link H-atom will be

connected. (For the 2nd qm region, qm/mm boundary will be

handled only by the H-link atom approach. However, the user

does not need to invoke ADDLink for this. The position will be

internally determined and the gradients are projected out.)

RCUT : cutoff distance for mm atoms that are included in the 2nd

qm/mm calcualtion.

**This is one nice way to include long-range electrostatics for the ab initio

qm/mm calculations, in which the long-range electrostatics are included at

the semiempirical level. For example, users can select the 1st qm region

to be same as the 2nd qm region, and specify RCUT for the 2nd qm region,

while the 1st qm region can be calculated with either QM/MM-Ewald sum or

no-cutoff.

Note: Currently, the SQUANTM module does not support UHF calculations.

Thus, if you want to run UHF calculations, use QUANTUM or MNDO97

module available for CHARMM QM/MM calculations.

For QM-MM interaction, the interaction doesn't include the

Gaussian core-core interactions in the PDDG/PM3 model

(refer future implementation and changes). However, in the AM1

and PM3 model, it is computed as default unless turned off

by using NOGAussian keyword. Depending on your keyword selection,

the results could be different from the original implementation in

QUANTUM or MNDO97 based on J. Comput. Chem. (1990) 6, 700.

Syntax for SQUANTM commands

QUANtum [atom-selection] [GLNK atom-selection]

[REMOve] [SWITched]

[AM1|PM3|MNDO|PDP3|PDMN] [CHARge int] [NOGAussian] [NDIS]

[SCFCriteria real]

[DOUBLET|TRIPLET]

[NEWD int] ewald-spec NOPMEwald

[DUALqm] { [PERTurbation pert-spec] }

{ [MLAYered mlay-spec] }

ewald-spec::= { [KMAX int] } [KSQMAX int]

{ [KMXX int] [KMXY int] [KMXZ int] }

pert-spec ::= [atom-selection] [KHARge int] [GLN2 atom-selection]

[REF0 real] [PEF1 real] [PEF2 real]

[TEMP real]

[PKAP] { [NOMM] }

{ [NOAN] [NODI] [NOIM] }

mlay-spec ::= [atom-selection] [KHARge int] [LINK atom-selection]

[RCUT real]

(**mlay-spec: refer the comments below.)

GLNK: GHO method implementation (refer qmmm.info).

REMOve: Classical energies within QM atoms are removed.

SWITched: Use switching function from CTONNB to CTOFNB values

based on GROUp method (refer nbonds.info). It is

incompatible with NEWD options

AM1|PM3|MNDO|PDP3|PDMN: AM1 model, PM3 model, MNDO model,

PDDG/PM3 (PDP3) model, and PDDG/MNDO (PDMN) model.

Note: currently, GHO method only support AM1 and

PM3 model.

For PDDG/PM3 and PDDG/MNDO model, the reference

is Repasky et al. J. Comput. Chem. (2002), 23, 1601.

NOGAussian: This will turn off Gaussian core-core interaction

between QM and MM pairs in the AM1 and PM3 model.

As a default, the Gaussian core-core interactions

will be computed.

NDIS : Turn off DIIS converger. (default is .false.)

NEWD and ewald-spec: refer the description for QUANTUM module.

NOPMEwald: Use regualr QM/MM-Ewald summation methods. (Default is false.)

This is added for backward compatibility. Note that only for

SQUANTM supports QM/MM-PME (refer details for NEWD description.)

DUALqm : Use dual qm/mm calculations. (Multiple qm/mm region

or FEP calculation.)

PERTurbation and pert-spec : Do FEP pKa calculations.

The reactant state (lambda=0) should be

the protonated state, and the product state

should be the deprotonated state (lambda=1).

The perturbation is only applied to the

electrostatic interactions between QM and

MM pairs.

H_eff = (1-lambda)*H_reactant + (lambda)*H_product

atom-selection: atom selection for the product state (lambda=1).

Mostly, this atom selection lacks the H atom that is

annihilated in the FEP calculations.

KHARge : charge for 2nd qm region (product state).

GLN2 : use GHO method in the 2nd qm region.

REF0/PEF1/PEF2/TEMP : refer section for "Description of the PERT Command"

(above).

PKAP : turn on mm valency terms for pKa calculation, in particular,

for dummy H-atom.

In the product state, the H atom (for the protonated state)

is changed into mm dummy atom that is not interact with other

atoms (mm and qm atoms) electrostatically, while the bond,

angle, dihedral, and improper terms are maintained to avoid

the end point problem during the FEP calculations. (Refer the

approach of Riccardi et al. J. Phys. Chem. B (2005), 105,

17715.)

NOMM : turn off the angle/dihedral/improper terms for dummy H-atom.

NOAN / NODI / NOIM : specifically turn off either angle, dihedral, or

improper terms.

("NOMM" is same as "NOAN NODI NOIM.")

**Note that the bond terms are maintained.**

MLAYered and mlay-spec: Do multi-layered qm/mm calculations.

This is similar to the electronically embedded ONIOM

type potential. The 1st qm/mm layer has a larger qm

selection, and the 2nd qm/mm layer has a smaller qm

selection but is a subset of the 1st qm selection.

The total energy is extrapolated from the ab initio

and semiempirical qm/mm calculations. Therefore, it

assumes the potential at the semiempirical level for

the larger qm region is corrected at the ab initio

level for the smaller qm region, and the 2nd qm region

should be chosen with care.

E_tot = {E_semi-qm/mm (1st qm/mm region)}

+ {E_ai-qm/mm (2nd qm/mm region) - E_semi-qm/mm (2nd qm/mm region)}

**Note that only GAMESS-UK is tested with SQUANTM, and check for future

update for GAMESS-US. To compile for this, use both U and SQ in the

install.com.

atom-selection: atom selection for the 2nd qm region. (This should be a subset

of 1st qm selection.)

KHARge : charge for the 2nd qm region.

LINK atom-sele: selection for (2nd) qm atoms to which the link H-atom will be

connected. (For the 2nd qm region, qm/mm boundary will be

handled only by the H-link atom approach. However, the user

does not need to invoke ADDLink for this. The position will be

internally determined and the gradients are projected out.)

RCUT : cutoff distance for mm atoms that are included in the 2nd

qm/mm calcualtion.

**This is one nice way to include long-range electrostatics for the ab initio

qm/mm calculations, in which the long-range electrostatics are included at

the semiempirical level. For example, users can select the 1st qm region

to be same as the 2nd qm region, and specify RCUT for the 2nd qm region,

while the 1st qm region can be calculated with either QM/MM-Ewald sum or

no-cutoff.

Note: Currently, the SQUANTM module does not support UHF calculations.

Thus, if you want to run UHF calculations, use QUANTUM or MNDO97

module available for CHARMM QM/MM calculations.

For QM-MM interaction, the interaction doesn't include the

Gaussian core-core interactions in the PDDG/PM3 model

(refer future implementation and changes). However, in the AM1

and PM3 model, it is computed as default unless turned off

by using NOGAussian keyword. Depending on your keyword selection,

the results could be different from the original implementation in

QUANTUM or MNDO97 based on J. Comput. Chem. (1990) 6, 700.

Top

Installation of SQUANTM module in CHARMM

To compile SQUANTM with CHARMM, one uses:

configure --with-squantm

make -C build/cmake install

The "--with-squantm" specifies to compile SQUANTM with CHARMM by replacing QUANTUM

keyword in pref.dat file. Currently, the platform should support

compilers that can compile F77 and F90 code simultaneously. The

platform and compilers tested include ALTIX and GNU using intel fortran

compilers (ifort and efc), and IBMAIX and IBMAIXMP platform using xlf90

and related compiler. For other platforms, install.com and Makefile

need to be modified accordingly.

Installation of SQUANTM module in CHARMM

To compile SQUANTM with CHARMM, one uses:

configure --with-squantm

make -C build/cmake install

The "--with-squantm" specifies to compile SQUANTM with CHARMM by replacing QUANTUM

keyword in pref.dat file. Currently, the platform should support

compilers that can compile F77 and F90 code simultaneously. The

platform and compilers tested include ALTIX and GNU using intel fortran

compilers (ifort and efc), and IBMAIX and IBMAIXMP platform using xlf90

and related compiler. For other platforms, install.com and Makefile

need to be modified accordingly.