# mndo97 (c49b1)

Combined Quantum Mechanical and Molecular Mechanics Method

Based on MNDO97 in CHARMM

by Paul Bash (pabash@nwu.edu)

Additional modifications

Kwangho Nam(nam@chem.umn.edu) and Darrin York

* Description | Description of the MNDO97 commands

* Usage | How to run MNDO97 in CHARMM

* NEWD | NEWD Command

* Installation | How to install MNDO97 in CHARMM environment

Based on MNDO97 in CHARMM

by Paul Bash (pabash@nwu.edu)

Additional modifications

Kwangho Nam(nam@chem.umn.edu) and Darrin York

* Description | Description of the MNDO97 commands

* Usage | How to run MNDO97 in CHARMM

* NEWD | NEWD Command

* Installation | How to install MNDO97 in CHARMM environment

Top

The MNDO97 QM potential is initialized with the MNDO97 command.

[SYNTAX MNDO97]

MNDO97 [REMOve] [EXGRoup] (atom selection)

[GLNK atom-selection]

[AM1|PM3|MNDO|MNDD|AMDD] [PHOT] [CHARge int]

[SWITched]

[DXLBomd] [NORDder int] [NSTEpscf int]

[D3BJ] [D3PARAM] [S6VA real] [S8VA real] [A1VA real] [A2VA real]

[H4CO] [PRED] [POHO real] [POHN real] [PNHO real] [PNHN real]

[MWHO real] [MNH4 real] [MCOO real]

[REPK real] [REPE real] [REPR real]

[NEWD int] ewald-spec [NOPMewald]

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

{ KMXX integer KMXY integer KMXZ integer }

REMOve: Classical energies within QM atoms are removed.

EXGRoup: QM/MM Electrostatics for link host groups removed.

GLNK: GHO method implementation (refer qmmm.info).

AM1: The AM1 method is to be used. (default)

PM3: The PM3 method is to be used.

MNDO: The MNDO method to be used.

MNDD: The MNDO/d method to be used.

AMDD: The AM1/d method to be used. (This method has very limited number of atoms

supported. Specifically, use in combination with PHOT keyword.)

PHOT: For the AM1/d method, PHOT use the AM1/d-PhoT method (Nam, JCTC, 2007).

Also, for Mg atom, it uses AM1 parameters.

CHARge: Total charge of QM region. (At present, it only supports RHF options.)

SWITched: Use the (group-based) switching function for the QM-MM interactions.

See below, if this option is used together with QM/MM-Ewald or QM/MM-PME

method.

DXLBomd: This uses the Niklasson JCP (2009) 130:214109 and Zheng JCT (2011) 135:044122,

in which the quess QM density is propagated using Dissipated Lagrandian MD.

The dissipation requires user to provide two variables. They are provided

using

NORDder : The maximum order to sum the dissipation terms. At present, only terms

between 3 and 9 are supported. See Niklasson JCP (2009) 130:214109.

NSTEpscf: The number of SCF cycle. Mostly, 7 or larger is safe. Also, in many cases

smaller than 7 SCF cycles provides stable MD simulations.

For details of the method, please refer Niklasson JCP (2009) 130:214109 and

Zheng JCT (2011) 135:044122.

D3BJ: Use Grimme's D3 dispersion method. The default is the two-body dispersion

correciton with Becky and Johsnson's damping function

(Grimme, JCC (2011) 32:1456)

D3PARAM: Use the user supplied D3-BJ parameters. Use the below to read user

provided parameters: S6VA, S8VA, A1VA, and A2VA

S6VA: s6 parameter. The scaling factor for the R^-6 term.

The default is 1.0 and it is advised not to change this value.

S8VA: s8 parameter. The scaling factor for the R^-8 term.

A1VA: a1 parameter. a1 and a2 are the two dampling parameters introducted by BJ.

A2VA: a2 parameter.

H4CO: Use of the H4 correction (Rezac, J Chem Theory Comput (2021) 8:141).

When it is used, it is recommended to use together with D3BJ correction.

Refer the reference for the default paramesters for AM1 and PM3 methods.

PRED: Use the user supplied H4 correction parameters:

POHO: C_OO parameter.

POHN: C_ON parameter.

PNHO: C_NO parameter.

PNHN: C_NN parameter.

MWHO: C_wat parameter.

MNH4: C_S,NHR3+ parameter.

MCOO: C_S,COO- parameter.

REPK: S_HH repulsion parameter in unit of kcal/mol.

See eq. (11) of the reference.

REPE: e_HH repulsion parameter.

REPR: r_0,HH repulsion parameter in unit of Angstrom.

Current implementation has a limit in choosing non-bonded options. All

atom based cutoffs methods is not fully supported for a certain boundary

conditions such as periodic boundary condition. In any case, the QM-MM

non-bond generation routine will only generate the non-bond list based

on group-group separation scheme. Especially to use any periodic boundary

conditions, use group based cutoff scheme.

The MNDO97 QM potential is initialized with the MNDO97 command.

[SYNTAX MNDO97]

MNDO97 [REMOve] [EXGRoup] (atom selection)

[GLNK atom-selection]

[AM1|PM3|MNDO|MNDD|AMDD] [PHOT] [CHARge int]

[SWITched]

[DXLBomd] [NORDder int] [NSTEpscf int]

[D3BJ] [D3PARAM] [S6VA real] [S8VA real] [A1VA real] [A2VA real]

[H4CO] [PRED] [POHO real] [POHN real] [PNHO real] [PNHN real]

[MWHO real] [MNH4 real] [MCOO real]

[REPK real] [REPE real] [REPR real]

[NEWD int] ewald-spec [NOPMewald]

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

{ KMXX integer KMXY integer KMXZ integer }

REMOve: Classical energies within QM atoms are removed.

EXGRoup: QM/MM Electrostatics for link host groups removed.

GLNK: GHO method implementation (refer qmmm.info).

AM1: The AM1 method is to be used. (default)

PM3: The PM3 method is to be used.

MNDO: The MNDO method to be used.

MNDD: The MNDO/d method to be used.

AMDD: The AM1/d method to be used. (This method has very limited number of atoms

supported. Specifically, use in combination with PHOT keyword.)

PHOT: For the AM1/d method, PHOT use the AM1/d-PhoT method (Nam, JCTC, 2007).

Also, for Mg atom, it uses AM1 parameters.

CHARge: Total charge of QM region. (At present, it only supports RHF options.)

SWITched: Use the (group-based) switching function for the QM-MM interactions.

See below, if this option is used together with QM/MM-Ewald or QM/MM-PME

method.

DXLBomd: This uses the Niklasson JCP (2009) 130:214109 and Zheng JCT (2011) 135:044122,

in which the quess QM density is propagated using Dissipated Lagrandian MD.

The dissipation requires user to provide two variables. They are provided

using

NORDder : The maximum order to sum the dissipation terms. At present, only terms

between 3 and 9 are supported. See Niklasson JCP (2009) 130:214109.

NSTEpscf: The number of SCF cycle. Mostly, 7 or larger is safe. Also, in many cases

smaller than 7 SCF cycles provides stable MD simulations.

For details of the method, please refer Niklasson JCP (2009) 130:214109 and

Zheng JCT (2011) 135:044122.

D3BJ: Use Grimme's D3 dispersion method. The default is the two-body dispersion

correciton with Becky and Johsnson's damping function

(Grimme, JCC (2011) 32:1456)

D3PARAM: Use the user supplied D3-BJ parameters. Use the below to read user

provided parameters: S6VA, S8VA, A1VA, and A2VA

S6VA: s6 parameter. The scaling factor for the R^-6 term.

The default is 1.0 and it is advised not to change this value.

S8VA: s8 parameter. The scaling factor for the R^-8 term.

A1VA: a1 parameter. a1 and a2 are the two dampling parameters introducted by BJ.

A2VA: a2 parameter.

H4CO: Use of the H4 correction (Rezac, J Chem Theory Comput (2021) 8:141).

When it is used, it is recommended to use together with D3BJ correction.

Refer the reference for the default paramesters for AM1 and PM3 methods.

PRED: Use the user supplied H4 correction parameters:

POHO: C_OO parameter.

POHN: C_ON parameter.

PNHO: C_NO parameter.

PNHN: C_NN parameter.

MWHO: C_wat parameter.

MNH4: C_S,NHR3+ parameter.

MCOO: C_S,COO- parameter.

REPK: S_HH repulsion parameter in unit of kcal/mol.

See eq. (11) of the reference.

REPE: e_HH repulsion parameter.

REPR: r_0,HH repulsion parameter in unit of Angstrom.

Current implementation has a limit in choosing non-bonded options. All

atom based cutoffs methods is not fully supported for a certain boundary

conditions such as periodic boundary condition. In any case, the QM-MM

non-bond generation routine will only generate the non-bond list based

on group-group separation scheme. Especially to use any periodic boundary

conditions, use group based cutoff scheme.

Top

Description of the NEWE Command

[ NEWD int ] ewald-spec [NOPMewald]

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

and Nam. JCTC (2014).

With NOPMewald, the regaular Ewald sum method is used for the QM/MM calculation.

So, this option is denoted as QM/MM-Ewald method. Without NOPMewald, if

the MM use PME method, the QM/MM part is also QM/MM-PME method. (» 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 CHARMM, it has no limitation on the shape of box, and can be

used with PMEwald 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.

When QM/MM-Ewald or QM/MM-PME method is used together with the SWITched option.

The total energy is expressed as

E_total = Sw(r)*E_qm/mm(real space) + dE_qm/mm(periodic correction) + E_mm

E_qm/mm(real space): The regular QM/MM interaction, in which MM point charges

interact with the entire QM (electron) density.

dE_qm/mm(periodic correction)

= (1-Sw(r))*dE_qm/mm (real space part) + dE_qm/mm(reciprocal space part)

where d= Dela.

For each term, refer Nam JCTC (2005) 1, 2, and Nam JCTC (2014) 10, 4175.

When this is used with the SWITched option, the real space is switched off at the

cutoff distance, and dE_qm/mm (real space part) is turned on slowly between the

cut on and cut off distances. This makes the transition from the full QM/MM real

space potential to the dE_qm/mm (real space part) correction smoothly and thus

generate more stable MD trajectory.

Description of the NEWE Command

[ NEWD int ] ewald-spec [NOPMewald]

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

and Nam. JCTC (2014).

With NOPMewald, the regaular Ewald sum method is used for the QM/MM calculation.

So, this option is denoted as QM/MM-Ewald method. Without NOPMewald, if

the MM use PME method, the QM/MM part is also QM/MM-PME method. (» 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 CHARMM, it has no limitation on the shape of box, and can be

used with PMEwald 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.

When QM/MM-Ewald or QM/MM-PME method is used together with the SWITched option.

The total energy is expressed as

E_total = Sw(r)*E_qm/mm(real space) + dE_qm/mm(periodic correction) + E_mm

E_qm/mm(real space): The regular QM/MM interaction, in which MM point charges

interact with the entire QM (electron) density.

dE_qm/mm(periodic correction)

= (1-Sw(r))*dE_qm/mm (real space part) + dE_qm/mm(reciprocal space part)

where d= Dela.

For each term, refer Nam JCTC (2005) 1, 2, and Nam JCTC (2014) 10, 4175.

When this is used with the SWITched option, the real space is switched off at the

cutoff distance, and dE_qm/mm (real space part) is turned on slowly between the

cut on and cut off distances. This makes the transition from the full QM/MM real

space potential to the dE_qm/mm (real space part) correction smoothly and thus

generate more stable MD trajectory.

Top

MNDO97/CHARMM interface status (February 1997)

- MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat

To compile MNDO97 with CHARMM one uses:

$ ./configure --with-mndo97 --without-colfft

$ make -C build/cmake install

The "--with-mndo97" specifies to compile and link MNDO97 with CHARMM.

MNDO97/CHARMM interface status (February 1997)

- MNDO97, CADPAC, GAMESS and QUANTUM keywords cannot coexist in pref.dat

To compile MNDO97 with CHARMM one uses:

$ ./configure --with-mndo97 --without-colfft

$ make -C build/cmake install

The "--with-mndo97" specifies to compile and link MNDO97 with CHARMM.