# energy (c39b1)

Energy Manipulations: Minimization and Dynamics

The main purpose of CHARMM is the evaluation and manipulation of

the potential energy of a macromolecular system. In order to compute

the energy, several conditions must be met. There are also several

support commands which directly relate to energy evaluation.

* Description | Description of the energy commands

* Skipe | Selection of particular energy terms

* Interaction | Computation of interaction energies and forces.

* Fast | Requirements for using the fast routines

* Needs | Requirements for all energy evaluations

* Optional | Optional actions to be taken beforehand

* Substitution | Command line energy substitution parameters

* Running Average | ESTATS command usage

* Multe | Multiple energy evaluation

The main purpose of CHARMM is the evaluation and manipulation of

the potential energy of a macromolecular system. In order to compute

the energy, several conditions must be met. There are also several

support commands which directly relate to energy evaluation.

* Description | Description of the energy commands

* Skipe | Selection of particular energy terms

* Interaction | Computation of interaction energies and forces.

* Fast | Requirements for using the fast routines

* Needs | Requirements for all energy evaluations

* Optional | Optional actions to be taken beforehand

* Substitution | Command line energy substitution parameters

* Running Average | ESTATS command usage

* Multe | Multiple energy evaluation

Top

Syntax for Energy Commands

There are two direct energy evaluation commands. One is parsed

through the minimization parser and the other involves a direct call

to GETE.

the forces are also obtained.

The ENERgy command. (processed through the minimization parser)

[SYNTAX ENERgy]

ENERgy [ nonbond-spec ] [ hbond-spec ] [ image-spec ] [ print-spec ]

[ domdec-spec ] [ COMP ] [ INBFrq 0 ] [ IHBFrq 0 ]

[ IMGFrq 0 ] [NOUPdate] [ openmm-spec ]

hbond-spec

nonbond-spec

image-spec

domdec-spec

openmm-spec

If the COMP keyword is specified, then the comparison coordinate

set is used, but this disables the use of the fast routines. The keyword

NOUPdate turns off all update routines, and thus requires all lists

to be present already.

The GETE command. (a direct call to GETE)

[SYNTAX GETEnergy]

GETE [ COMP ] [ PRINt [ UNIT int ] ] [ openmm-spec ]

[ NOPRint ]

For this command to work, all list must be set up. This is best done

through the UPDAte command. The COMP keyword will cause the comparison

coordinate set to be used. The PRINt keyword will result in a subsequent

call to PRINTE in order to print the energy. If the PRINt keyword is not

specified, then NO indication that the energy has been called will be given.

The UPDAte command (sets up required lists for GETE)

[SYNTAX UPDAte lists]

UPDAte [ nonbond-spec ] [ hbond-spec ] [ image-spec ] [ COMP ]

[ INBFrq 0 ] [ IHBFrq 0 ] [ IMGfrq 0 ]

[ EXSG {list-of-segment-names} | EXOF ]

The update command will set up the codes lists and also create a

nonbond list (unless INBFrq is 0) and a new hbond list (unless IHBFrq is 0).

If the COMP keyword is specified, then the comparison coordinates will be

used in setting up the nonbond and hbond lists.

EXSG keword with optional following list of segment names allows to

exclude some nonbonded interactions (ELEC & VDW). If list of names is empty

ALL INTERsegment nonbonded interactions will be excluded. If list is not

empty all INTER and INTRA segment nonbonded interactions for listed

segments will be ecluded. EXOF turns off this option.

H-bond energies (HBON) are not affected at the moment (Dec 3, 1991).

Syntax for Energy Commands

There are two direct energy evaluation commands. One is parsed

through the minimization parser and the other involves a direct call

to GETE.

**»**minimiz and**»**usage interface. In addition to getting the energy,the forces are also obtained.

The ENERgy command. (processed through the minimization parser)

[SYNTAX ENERgy]

ENERgy [ nonbond-spec ] [ hbond-spec ] [ image-spec ] [ print-spec ]

[ domdec-spec ] [ COMP ] [ INBFrq 0 ] [ IHBFrq 0 ]

[ IMGFrq 0 ] [NOUPdate] [ openmm-spec ]

hbond-spec

**»**hbonds .nonbond-spec

**»**nbonds .image-spec

**»**images Update.domdec-spec

**»**domdec .openmm-spec

**»**openmm .If the COMP keyword is specified, then the comparison coordinate

set is used, but this disables the use of the fast routines. The keyword

NOUPdate turns off all update routines, and thus requires all lists

to be present already.

The GETE command. (a direct call to GETE)

[SYNTAX GETEnergy]

GETE [ COMP ] [ PRINt [ UNIT int ] ] [ openmm-spec ]

[ NOPRint ]

For this command to work, all list must be set up. This is best done

through the UPDAte command. The COMP keyword will cause the comparison

coordinate set to be used. The PRINt keyword will result in a subsequent

call to PRINTE in order to print the energy. If the PRINt keyword is not

specified, then NO indication that the energy has been called will be given.

The UPDAte command (sets up required lists for GETE)

[SYNTAX UPDAte lists]

UPDAte [ nonbond-spec ] [ hbond-spec ] [ image-spec ] [ COMP ]

[ INBFrq 0 ] [ IHBFrq 0 ] [ IMGfrq 0 ]

[ EXSG {list-of-segment-names} | EXOF ]

The update command will set up the codes lists and also create a

nonbond list (unless INBFrq is 0) and a new hbond list (unless IHBFrq is 0).

If the COMP keyword is specified, then the comparison coordinates will be

used in setting up the nonbond and hbond lists.

EXSG keword with optional following list of segment names allows to

exclude some nonbonded interactions (ELEC & VDW). If list of names is empty

ALL INTERsegment nonbonded interactions will be excluded. If list is not

empty all INTER and INTRA segment nonbonded interactions for listed

segments will be ecluded. EXOF turns off this option.

H-bond energies (HBON) are not affected at the moment (Dec 3, 1991).

Top

Skipping selected energy terms

There is a facility to skip any desired energy terms during

energy evaluation. For each energy term there is associated a logical

flag determining whether that energy term is to be computed.

Specifications are processed sequentially. The default operation

is INCLude which implies that subsequent energy term are to be removed

from the energy calculation. NOTE: that EXCLude implies that the

energy term is to be computed.

If for some reason, the list presented here is out of date, the

data in SKIPE(energy.src) and in ENER.FCM of the source should be

consulted.

Syntax:

[SYNTAX SKIP energy terms]

[ INCLude ]

[ EXCLude ]

SKIPe repeat( [ ALL ] )

[ NONE ]

[ item ]

item::=

[ BOND ] [ ANGL ] [ UREY ] [ DIHE ]

[ IMPR ] [ VDW ] [ ELEC ] [ HBON ]

[ USER ] [ HARM ] [ CDIH ] [ CIC ]

[ CDRO ] [ NOE ] [ SBOU ] [ IMNB ]

[ IMEL ] [ IMHB ] [ XTLV ] [ XTLE ]

[ EXTE ] [ RXNF ] [ ST2 ] [ IMST ]

[ TSM ] [ QMEL ] [ QMVDW] [ ASP ]

[ EHARM] [ GEO ] [ MDIP ] [ STRB ]

[ VATT ] [ VREP ] [ IMVREP ] [IMVATT]

[ OOPL ] [ CMAP ] [ EPOL ] [ CPUC ]

description:

BOND - bond energy

ANGL - angle energy

UREY - Urey-Bradley energy term

DIHE - dihedral energy

IMPR - improper dihedral energy

VDW - van der Waal energy

ELEC - electrostatic energy

HBON - hydrogen bond energy

USER - user supplied energy (USERLINK)

HARM - harmonic positional constraint energy

CDIH - constrained dihedral energy

CPUC - constrained puckering energy

CIC - internal coordinate constraint energy

CDRO - quartic droplet potential energy

NOE - NOE general distance restraints

SBOU - solvent boundary energy

IMNB - image van der Waal energy

IMEL - image electrostatic energy

IMHB - image hydrogen bond energy

XTLV - crystal van der Waal energy

XTLE - crystal electrostatic energy

EXTE - extended electrostatic energy

RXNF - reaction field energy

ST2 - ST2 water-water energy

IMST - image ST2 water-water energy

TSM - TMS free energy term.

QMEL - energy for the quantum mechanical atoms and their

electrostatic interactions with the MM atoms using the AM1

or MNDO semi-empirical approximations

QMVDW - van der Waals energy between the quantum mechanical and

molecular mechanical atoms

ASP - solvation free energy term based on Wesson and Eisenberg

surface area method

EHARM - second harmonic restraint term (for implicit Euler integration)

GEO - Mean-Field-Potential energy

MDIP - MDIPole mean fields constraints

STRB - strech-bend interaction (MMFF)

VATT - VdW attraction (MMFF)

VREP - VdW repulsion (MMFF)

IMVREP - image VdW repulsion (MMFF)

IMVATT - image VdW attraction (MMFF)

OOPL - out-of-plane (MMFF)

CMAP - 2D dihedral cross term energy correction map

EPOL - polarization energy computed from PIPF (» pipf )

Examples;

SKIP ALL EXCL BOND - do just bond energy

SKIP EXCL ALL - return flags to default state

SKIP ELEC VDW - throw out electrostatics and van der Waals energy

Skipping selected energy terms

There is a facility to skip any desired energy terms during

energy evaluation. For each energy term there is associated a logical

flag determining whether that energy term is to be computed.

Specifications are processed sequentially. The default operation

is INCLude which implies that subsequent energy term are to be removed

from the energy calculation. NOTE: that EXCLude implies that the

energy term is to be computed.

If for some reason, the list presented here is out of date, the

data in SKIPE(energy.src) and in ENER.FCM of the source should be

consulted.

Syntax:

[SYNTAX SKIP energy terms]

[ INCLude ]

[ EXCLude ]

SKIPe repeat( [ ALL ] )

[ NONE ]

[ item ]

item::=

[ BOND ] [ ANGL ] [ UREY ] [ DIHE ]

[ IMPR ] [ VDW ] [ ELEC ] [ HBON ]

[ USER ] [ HARM ] [ CDIH ] [ CIC ]

[ CDRO ] [ NOE ] [ SBOU ] [ IMNB ]

[ IMEL ] [ IMHB ] [ XTLV ] [ XTLE ]

[ EXTE ] [ RXNF ] [ ST2 ] [ IMST ]

[ TSM ] [ QMEL ] [ QMVDW] [ ASP ]

[ EHARM] [ GEO ] [ MDIP ] [ STRB ]

[ VATT ] [ VREP ] [ IMVREP ] [IMVATT]

[ OOPL ] [ CMAP ] [ EPOL ] [ CPUC ]

description:

BOND - bond energy

ANGL - angle energy

UREY - Urey-Bradley energy term

DIHE - dihedral energy

IMPR - improper dihedral energy

VDW - van der Waal energy

ELEC - electrostatic energy

HBON - hydrogen bond energy

USER - user supplied energy (USERLINK)

HARM - harmonic positional constraint energy

CDIH - constrained dihedral energy

CPUC - constrained puckering energy

CIC - internal coordinate constraint energy

CDRO - quartic droplet potential energy

NOE - NOE general distance restraints

SBOU - solvent boundary energy

IMNB - image van der Waal energy

IMEL - image electrostatic energy

IMHB - image hydrogen bond energy

XTLV - crystal van der Waal energy

XTLE - crystal electrostatic energy

EXTE - extended electrostatic energy

RXNF - reaction field energy

ST2 - ST2 water-water energy

IMST - image ST2 water-water energy

TSM - TMS free energy term.

QMEL - energy for the quantum mechanical atoms and their

electrostatic interactions with the MM atoms using the AM1

or MNDO semi-empirical approximations

QMVDW - van der Waals energy between the quantum mechanical and

molecular mechanical atoms

ASP - solvation free energy term based on Wesson and Eisenberg

surface area method

EHARM - second harmonic restraint term (for implicit Euler integration)

GEO - Mean-Field-Potential energy

MDIP - MDIPole mean fields constraints

STRB - strech-bend interaction (MMFF)

VATT - VdW attraction (MMFF)

VREP - VdW repulsion (MMFF)

IMVREP - image VdW repulsion (MMFF)

IMVATT - image VdW attraction (MMFF)

OOPL - out-of-plane (MMFF)

CMAP - 2D dihedral cross term energy correction map

EPOL - polarization energy computed from PIPF (» pipf )

Examples;

SKIP ALL EXCL BOND - do just bond energy

SKIP EXCL ALL - return flags to default state

SKIP ELEC VDW - throw out electrostatics and van der Waals energy

Top

Interaction energies and forces

The INTEraction command computes the energy and forces

between any two selections of atoms.

[SYNTAX INTEraction energy]

INTEraction [ COMP ] [ NOPRint ] 2x(atom-selection) [UNIT int]

If only one atom selection is given, then a self energy will be computed.

This routine is quite efficient and may be used within a Charmm loop

without too much overhead, though there are some restrictions.

The COMP keyword causes the comparicon coordinates to be used.

The NOPRint keyword will prevent the results from being printed.

This routine works in the same manner as the GETE command in that

all of the lists (CODES, nonbond, and Hbond) must be specified before

invoking this command. One difference is that SHAKE will not be respected

with this command (i.e. if the coordinates don't satisfy the constraints,

neither will the energy).

The following energy terms may be computed by this routine

(unless supressed with the SKIP command);

Bond - Energy defined by the two atoms involved.

Angles - Energy allocated to the central atom (auto energy only).

Dihedral - Energy defined between central two atoms

Improper - Energy defined by first atom (auto energy only)

van der Waal - ATOM option only. Energy defined by two atoms involved.

Electrostatic - ATOM option only. Energy defined by two atoms involved.

Hbond - Energy defined by heavy atom donor and acceptor atom.

Harmonic cons - Energy allocated to central atom (auto energy only).

Dihedral cons - Energy defined by central two atoms.

User energy - Atom selections may be passed to USERE in the selection

common (DEFIne command). Fill forces and energies as desired.

All other energy terms will be zeroed. For terms listed "auto energy only",

the corresponding atom must be present in both atom selections.

For the remaining terms, one atom of the pair must be present in each

of the atom selections. The energy division matches the method used in

the analysis facility.

This command will not work with the selection of images atoms,

or the selection of ST2 waters. All energy terms not listed above will

not be computed. The nonbond list must be generated with the ATOM and VATOM

options. [T.Lazaridis, July 1999: Now INTE can work with the GROUP option]

The individual energy terms are stored in the energy common

and are available in commands and titles via the "?energy-term"

substitution.

The forces for all kept energy terms will be returned in

the force arrays. Note, that it is possible for atoms to have a force

that were not selected in either selection specification. This may

happen for angle or dihedral terms on the first and last atoms. It may

also happen in a similar manner for improper dihedrals, hydrogen bonding

terms, and dihedral constraints.

Interaction energies and forces

The INTEraction command computes the energy and forces

between any two selections of atoms.

[SYNTAX INTEraction energy]

INTEraction [ COMP ] [ NOPRint ] 2x(atom-selection) [UNIT int]

If only one atom selection is given, then a self energy will be computed.

This routine is quite efficient and may be used within a Charmm loop

without too much overhead, though there are some restrictions.

The COMP keyword causes the comparicon coordinates to be used.

The NOPRint keyword will prevent the results from being printed.

This routine works in the same manner as the GETE command in that

all of the lists (CODES, nonbond, and Hbond) must be specified before

invoking this command. One difference is that SHAKE will not be respected

with this command (i.e. if the coordinates don't satisfy the constraints,

neither will the energy).

The following energy terms may be computed by this routine

(unless supressed with the SKIP command);

Bond - Energy defined by the two atoms involved.

Angles - Energy allocated to the central atom (auto energy only).

Dihedral - Energy defined between central two atoms

Improper - Energy defined by first atom (auto energy only)

van der Waal - ATOM option only. Energy defined by two atoms involved.

Electrostatic - ATOM option only. Energy defined by two atoms involved.

Hbond - Energy defined by heavy atom donor and acceptor atom.

Harmonic cons - Energy allocated to central atom (auto energy only).

Dihedral cons - Energy defined by central two atoms.

User energy - Atom selections may be passed to USERE in the selection

common (DEFIne command). Fill forces and energies as desired.

All other energy terms will be zeroed. For terms listed "auto energy only",

the corresponding atom must be present in both atom selections.

For the remaining terms, one atom of the pair must be present in each

of the atom selections. The energy division matches the method used in

the analysis facility.

This command will not work with the selection of images atoms,

or the selection of ST2 waters. All energy terms not listed above will

not be computed. The nonbond list must be generated with the ATOM and VATOM

options. [T.Lazaridis, July 1999: Now INTE can work with the GROUP option]

The individual energy terms are stored in the energy common

and are available in commands and titles via the "?energy-term"

substitution.

The forces for all kept energy terms will be returned in

the force arrays. Note, that it is possible for atoms to have a force

that were not selected in either selection specification. This may

happen for angle or dihedral terms on the first and last atoms. It may

also happen in a similar manner for improper dihedrals, hydrogen bonding

terms, and dihedral constraints.

Top

The 10-12 van der Waals potential

The ETEN command is used to switch between the use of a 6-12 van der

Waals potential (default), and a 10-12 potential.

[SYNTAX ETEN ]

ETEN {ON}

{OFF}

Setting the flag "ETEN" to "ON or OFF" switches the van der Waals to

a modified Lennard-Jones function containing an attractive r^-10 term and

repulsive r^-12 and r^-6 terms. This was introduced to support simulation of

the Go models built by the webserver at

mmtsb.scripps.edu/webservices/gomodel.html

When the 10-12 potential is turned on, all energy evaluations will be

carried out using this potential, including minimizations, normal mode

analysis, etc. Issuing the ETEN command with any keyword other than ON will

turn off the 10-12 potential, reverting to the 6-12 potential.

The 10-12 potential energy may be turned off without reverting to the

6-12 potential using the SKIPE command with the VDW item, since this potential

replaces the VDW energy.

This option does not support CFF, MMFF, IMAGE, GRAPE, ewald, multi-

body dynamics, and fast vector. It also does not does not support van der

Waals shifting, force switching, or switching, as well as soft core van der

Waals.

This option fully supports BLOCK.

The 10-12 van der Waals potential

The ETEN command is used to switch between the use of a 6-12 van der

Waals potential (default), and a 10-12 potential.

[SYNTAX ETEN ]

ETEN {ON}

{OFF}

Setting the flag "ETEN" to "ON or OFF" switches the van der Waals to

a modified Lennard-Jones function containing an attractive r^-10 term and

repulsive r^-12 and r^-6 terms. This was introduced to support simulation of

the Go models built by the webserver at

mmtsb.scripps.edu/webservices/gomodel.html

When the 10-12 potential is turned on, all energy evaluations will be

carried out using this potential, including minimizations, normal mode

analysis, etc. Issuing the ETEN command with any keyword other than ON will

turn off the 10-12 potential, reverting to the 6-12 potential.

The 10-12 potential energy may be turned off without reverting to the

6-12 potential using the SKIPE command with the VDW item, since this potential

replaces the VDW energy.

This option does not support CFF, MMFF, IMAGE, GRAPE, ewald, multi-

body dynamics, and fast vector. It also does not does not support van der

Waals shifting, force switching, or switching, as well as soft core van der

Waals.

This option fully supports BLOCK.

Top

[SYNTAX FASTer ]

FASTer {integer}

{OFF }

{ON }

{DEFAult}

{SCALar } ! for testing only

{VECTor } ! for testing only

{CRAYvec } ! Use parallel code designed for a CRAY

{PARVec } ! Use parallel/vector code best SMP machines and Convex

Instead of using an integer value, FASTer command can be issued

with one of the following keywords.

Keyword Equivalent integer

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

FASTer OFF -1

DEFAult 0

ON 1

SCALar 2

The FASTer keyword or integer defines which versions of the energy routines

to be used.

FASTer -1 : Always use slow routines

FASTer 0 : Use fast routine if possible, no error if cannot (default)

FASTer 1 : Use best optimized routine for the current machine

(Error message if cannot)

FASTer 2 : Use fast scalar routine (Error message if cannot)

There exist a general and a fast version of the internal

energy routines (bond, angle, dihedral, and improper dihedral). The

is also a fast version of nonbond energy evaluation (roughly 30-50%

faster). These routines were designed for long minimization or

dynamics calculations.

To request the FAST routine, the FASTer command should be used

with a positive integer or an appropriate keyword. A negative

integer will disable the fast energy routines. If the fast routines

are requested and it is not possible to use the fast routines, a

warning will be issued, and the general routines will be used in their

place.

The fast routines are more efficient in several ways;

(1) arrays are included in common files rather than passed

(2) second derivatives have been removed

(3) analysis and print options have been removed

The restrictions are that;

(1) the MAIN coordinate set must be used in the energy evaluations

(2) second derivatives may not be requested

(3) The PSF, parameter, and codes arrays must be used (from the common files)

(4) a limited set of nonbond options must be used.

The current nonbond options supported by the fast nonbond routine

are as follows.

ATOM [CDIE] [SHIFt ] VATOM [VSHIft ]

[RDIE] [SWITch ] [VSWItch ]

[FSWItch] [VFSWitch]

[FSHIft ]

GROUP [CDIE] [SWITch ] VGROUP [VSWItch ]

[RDIE] [FSWItch]

[SYNTAX FASTer ]

FASTer {integer}

{OFF }

{ON }

{DEFAult}

{SCALar } ! for testing only

{VECTor } ! for testing only

{CRAYvec } ! Use parallel code designed for a CRAY

{PARVec } ! Use parallel/vector code best SMP machines and Convex

Instead of using an integer value, FASTer command can be issued

with one of the following keywords.

Keyword Equivalent integer

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

FASTer OFF -1

DEFAult 0

ON 1

SCALar 2

The FASTer keyword or integer defines which versions of the energy routines

to be used.

FASTer -1 : Always use slow routines

FASTer 0 : Use fast routine if possible, no error if cannot (default)

FASTer 1 : Use best optimized routine for the current machine

(Error message if cannot)

FASTer 2 : Use fast scalar routine (Error message if cannot)

There exist a general and a fast version of the internal

energy routines (bond, angle, dihedral, and improper dihedral). The

is also a fast version of nonbond energy evaluation (roughly 30-50%

faster). These routines were designed for long minimization or

dynamics calculations.

To request the FAST routine, the FASTer command should be used

with a positive integer or an appropriate keyword. A negative

integer will disable the fast energy routines. If the fast routines

are requested and it is not possible to use the fast routines, a

warning will be issued, and the general routines will be used in their

place.

The fast routines are more efficient in several ways;

(1) arrays are included in common files rather than passed

(2) second derivatives have been removed

(3) analysis and print options have been removed

The restrictions are that;

(1) the MAIN coordinate set must be used in the energy evaluations

(2) second derivatives may not be requested

(3) The PSF, parameter, and codes arrays must be used (from the common files)

(4) a limited set of nonbond options must be used.

The current nonbond options supported by the fast nonbond routine

are as follows.

ATOM [CDIE] [SHIFt ] VATOM [VSHIft ]

[RDIE] [SWITch ] [VSWItch ]

[FSWItch] [VFSWitch]

[FSHIft ]

GROUP [CDIE] [SWITch ] VGROUP [VSWItch ]

[RDIE] [FSWItch]

Top

Requirements before energy manipulations can take place

Before the energy of a system can be evaluated and manipulated,

a number of data structures must be present.

First, a PSF must be present.

Second, a parameter set must be present. It must contain all

parameters which are required by the PSF being used.

Third, coordinates must be defined for every atom in the system.

An undefined coordinate has a particular value, and if two coordinates

have the same value, division by zero will occur in the evaluation of

the energy. If the positions of hydrogens are required, the hydrogen

bond generation routine,

called before the energy is evaluated.

Fourth, provisions must be made for having a hydrogen bond list

and a non-bonded interaction list. Having non-zero frequencies for

updating this lists is one way, one can also read these lists in, see

commands,

Requirements before energy manipulations can take place

Before the energy of a system can be evaluated and manipulated,

a number of data structures must be present.

First, a PSF must be present.

Second, a parameter set must be present. It must contain all

parameters which are required by the PSF being used.

Third, coordinates must be defined for every atom in the system.

An undefined coordinate has a particular value, and if two coordinates

have the same value, division by zero will occur in the evaluation of

the energy. If the positions of hydrogens are required, the hydrogen

bond generation routine,

**»**hbonds must becalled before the energy is evaluated.

Fourth, provisions must be made for having a hydrogen bond list

and a non-bonded interaction list. Having non-zero frequencies for

updating this lists is one way, one can also read these lists in, see

**»**io read, or generate them with separatecommands,

**»**hbonds or**»**nbonds .Top

Optional actions you can take to modify the energy manipulations

There exist several commands which can modify the way the

potential energy is calculated or can affect the way energy

manipulations are performed.

The Constraint command,

be used to constraints of various kinds. First, it can be used to set

flags for particular atoms which will prevent them from being moved

during minimization or dynamics. Second, it can be used to add

positional constraint term to the potential energy. This term will be

harmonic about some reference position. The user is free to set the

force constant. Third, the user can place a harmonic constraint on the

value of particular torsion angles in an attempt to force the geometry

of a molecule. Other constraints are also available.

The SHAKe command,

used to set constraints on bond lengths and also bond angles during

dynamics. It is very valuable in that it permits a larger step size to

be used during dynamics. This is vital for dynamics where hydrogens

are explicitly represented as the low mass and high force constant of

bonds involving hydrogen require a ridiculously small step size.

The user interface commands can be used to modify the

calculation of the potential and to add another term to the potential

energy.

Optional actions you can take to modify the energy manipulations

There exist several commands which can modify the way the

potential energy is calculated or can affect the way energy

manipulations are performed.

The Constraint command,

**»**cons canbe used to constraints of various kinds. First, it can be used to set

flags for particular atoms which will prevent them from being moved

during minimization or dynamics. Second, it can be used to add

positional constraint term to the potential energy. This term will be

harmonic about some reference position. The user is free to set the

force constant. Third, the user can place a harmonic constraint on the

value of particular torsion angles in an attempt to force the geometry

of a molecule. Other constraints are also available.

The SHAKe command,

**»**cons SHAKE, isused to set constraints on bond lengths and also bond angles during

dynamics. It is very valuable in that it permits a larger step size to

be used during dynamics. This is vital for dynamics where hydrogens

are explicitly represented as the low mass and high force constant of

bonds involving hydrogen require a ridiculously small step size.

The user interface commands can be used to modify the

calculation of the potential and to add another term to the potential

energy.

**»**usage interface for details.Top

The following command line substitution values may be included in

any command or title. To get the total energy, the syntax;

...... ?TOTE .....

should be used.

Energy related properties:

'TOTE' - total energy

'TOTK' - total kinetic energy

'ENER' - total potential energy

'TEMP' - temperature (from KE)

'GRMS' - rms gradient

'BPRE' - boundary pressure applied

'VTOT' - total verlet energy (no HFC)

'VKIN' - total verlet kinetic energy (no HFC)

'EHFC' - high frequency correction energy

'EHYS' - slow growth hysteresis energy correction

'VOLU' - the volume of the primitive unit cell

= A.(B x C)/XNSYMM. Defined only if images are present,

or unless specified with the VOLUme keyword.

'PRSE' - the pressure calculated from the external virial.

'PRSI' - the pressure calculated from the internal virial.

'VIRE' - the external virial.

'VIRI' - the internal virial.

'VIRK' - the virial "kinetic energy".

Energy term names:

'BOND' - bond (1-2) energy

'ANGL' - angle (1-3) energy

'UREY' - additional 1-3 urey bradley energy

'DIHE' - dihedral 1-4 energy

'IMPR' - improper planar of chiral energy

'CMAP' - 2D dihedral cross term energy correction map

'STRB' - Strech-Bend coupling energy (MMFF)

'OOPL' - Out-off-plane energy (MMFF)

'VDW ' - van der waal energy

'ELEC' - electrostatic energy

'HBON' - hydrogen bonding energy

'USER' - user supplied energy term

'HARM' - harmonic positional restraint energy

'CDIH' - dihedral restraint energy

'CPUC' - puckering restraint energy

'CIC ' - internal coordinate restraint energy

'CDRO' - droplet restraint energy (approx const press)

'NOE' - general distance restraint energy (for NOE)

'SBOU' - solvent boundary lookup table energy

'IMNB' - primary-image van der waal energy

'IMEL' - primary-image electrostatic energy

'IMHB' - primary-image hydrogen bond energy

'EXTE' - extended electrostatic energy

'EWKS' - Ewald k-space sum energy term

'EWSE' - Ewald self energy term

'RXNF' - reaction field electrostatic energy

'ST2' - ST2 water-water energy

'IMST' - primary-image ST2 water-water energy

'TSM' - TMS free energy term

'QMEL' - Quantum (QM) energy with QM/MM electrostatics

'QMVD' - Quantum (QM/MM) van der Waal term

'ASP' - Atomic solvation parameter (surface) energy

'EHAR' - Restraint term for Implicit Euler integration

'GEO ' - Mean-Field-Potential energy term

'MDIP' - Dipole Mean-Field-Potential energy term

'PRMS' - Replica/Path RMS deviation energy

'PANG' - Replica/Path RMS angle deviation energy

'SSBP' - ??????? (undocumented)

'BK4D' - 4-D energy

'SHEL' - ??????? (undocumented)

'RESD' - Restrained Distance energy

'SHAP' - Shape restraint energy

'PULL' - Pulling force energy

'POLA' - Polarizable water energy

'DMC ' - Distance map restraint energy

'RGY ' - Radius of Gyration restraint energy

'EWEX' - Ewald exclusion correction energy

'EWQC' - Ewald total charge correction energy

'EWUT' - Ewald utility energy term (for misc. corrections)

Energy Pressure/Virial Terms:

'VEXX' - External Virial

'VEXY' -

'VEXZ' -

'VEYX' -

'VEYY' -

'VEYZ' -

'VEZX' -

'VEZY' -

'VEZZ' -

'VIXX' - Internal Virial

'VIXY' -

'VIXZ' -

'VIYX' -

'VIYY' -

'VIYZ' -

'VIZX' -

'VIZY' -

'VIZZ' -

'PEXX' - External Pressure

'PEXY' -

'PEXZ' -

'PEYX' -

'PEYY' -

'PEYZ' -

'PEZX' -

'PEZY' -

'PEZZ' -

'PIXX' - Internal Pressure

'PIXY' -

'PIXZ' -

'PIYX' -

'PIYY' -

'PIYZ' -

'PIZX' -

'PIZY' -

'PIZZ' -

Examples:

1. Save the structure with a lower NOE restraint energy.

READ COOR CARD UNIT 1 ! Read the first structure

READ COOR CARD COMP UNIT 2 ! Read the second structure

ENERGY ! Compute energy of first structure

SET 1 ?NOE ! save the NOE energy value

ENERGY COMP ! Compute the energy of the second structure

IF ?NOE LT @1 COOR COPY ! replace first structure if second has

! a lower energy.

2. Write some energy values when saving coordinates

....

COOR ORIE RMS MASS

ENERGY

OPEN WRITE CARD UNIT 22 NAME RESULT.CRD

WRITE COOR CARD UNIT 22

* Final coordinates

* energy=?ENER and electrostatic energy=?ELEC

* mass weighted rms deviation from xray structure is ?RMS

The following command line substitution values may be included in

any command or title. To get the total energy, the syntax;

...... ?TOTE .....

should be used.

Energy related properties:

'TOTE' - total energy

'TOTK' - total kinetic energy

'ENER' - total potential energy

'TEMP' - temperature (from KE)

'GRMS' - rms gradient

'BPRE' - boundary pressure applied

'VTOT' - total verlet energy (no HFC)

'VKIN' - total verlet kinetic energy (no HFC)

'EHFC' - high frequency correction energy

'EHYS' - slow growth hysteresis energy correction

'VOLU' - the volume of the primitive unit cell

= A.(B x C)/XNSYMM. Defined only if images are present,

or unless specified with the VOLUme keyword.

'PRSE' - the pressure calculated from the external virial.

'PRSI' - the pressure calculated from the internal virial.

'VIRE' - the external virial.

'VIRI' - the internal virial.

'VIRK' - the virial "kinetic energy".

Energy term names:

'BOND' - bond (1-2) energy

'ANGL' - angle (1-3) energy

'UREY' - additional 1-3 urey bradley energy

'DIHE' - dihedral 1-4 energy

'IMPR' - improper planar of chiral energy

'CMAP' - 2D dihedral cross term energy correction map

'STRB' - Strech-Bend coupling energy (MMFF)

'OOPL' - Out-off-plane energy (MMFF)

'VDW ' - van der waal energy

'ELEC' - electrostatic energy

'HBON' - hydrogen bonding energy

'USER' - user supplied energy term

'HARM' - harmonic positional restraint energy

'CDIH' - dihedral restraint energy

'CPUC' - puckering restraint energy

'CIC ' - internal coordinate restraint energy

'CDRO' - droplet restraint energy (approx const press)

'NOE' - general distance restraint energy (for NOE)

'SBOU' - solvent boundary lookup table energy

'IMNB' - primary-image van der waal energy

'IMEL' - primary-image electrostatic energy

'IMHB' - primary-image hydrogen bond energy

'EXTE' - extended electrostatic energy

'EWKS' - Ewald k-space sum energy term

'EWSE' - Ewald self energy term

'RXNF' - reaction field electrostatic energy

'ST2' - ST2 water-water energy

'IMST' - primary-image ST2 water-water energy

'TSM' - TMS free energy term

'QMEL' - Quantum (QM) energy with QM/MM electrostatics

'QMVD' - Quantum (QM/MM) van der Waal term

'ASP' - Atomic solvation parameter (surface) energy

'EHAR' - Restraint term for Implicit Euler integration

'GEO ' - Mean-Field-Potential energy term

'MDIP' - Dipole Mean-Field-Potential energy term

'PRMS' - Replica/Path RMS deviation energy

'PANG' - Replica/Path RMS angle deviation energy

'SSBP' - ??????? (undocumented)

'BK4D' - 4-D energy

'SHEL' - ??????? (undocumented)

'RESD' - Restrained Distance energy

'SHAP' - Shape restraint energy

'PULL' - Pulling force energy

'POLA' - Polarizable water energy

'DMC ' - Distance map restraint energy

'RGY ' - Radius of Gyration restraint energy

'EWEX' - Ewald exclusion correction energy

'EWQC' - Ewald total charge correction energy

'EWUT' - Ewald utility energy term (for misc. corrections)

Energy Pressure/Virial Terms:

'VEXX' - External Virial

'VEXY' -

'VEXZ' -

'VEYX' -

'VEYY' -

'VEYZ' -

'VEZX' -

'VEZY' -

'VEZZ' -

'VIXX' - Internal Virial

'VIXY' -

'VIXZ' -

'VIYX' -

'VIYY' -

'VIYZ' -

'VIZX' -

'VIZY' -

'VIZZ' -

'PEXX' - External Pressure

'PEXY' -

'PEXZ' -

'PEYX' -

'PEYY' -

'PEYZ' -

'PEZX' -

'PEZY' -

'PEZZ' -

'PIXX' - Internal Pressure

'PIXY' -

'PIXZ' -

'PIYX' -

'PIYY' -

'PIYZ' -

'PIZX' -

'PIZY' -

'PIZZ' -

Examples:

1. Save the structure with a lower NOE restraint energy.

READ COOR CARD UNIT 1 ! Read the first structure

READ COOR CARD COMP UNIT 2 ! Read the second structure

ENERGY ! Compute energy of first structure

SET 1 ?NOE ! save the NOE energy value

ENERGY COMP ! Compute the energy of the second structure

IF ?NOE LT @1 COOR COPY ! replace first structure if second has

! a lower energy.

2. Write some energy values when saving coordinates

....

COOR ORIE RMS MASS

ENERGY

OPEN WRITE CARD UNIT 22 NAME RESULT.CRD

WRITE COOR CARD UNIT 22

* Final coordinates

* energy=?ENER and electrostatic energy=?ELEC

* mass weighted rms deviation from xray structure is ?RMS

Top

Running Energy Averages (ESTATS)

The ESTATS command is a basic statistical facility that allows the

calculation and manipulation of the mean and variance of the potential

energy and its components over a number of potential energy calculations,

without the need for writing out trajectories or coordinate files--i.e.

the calculations are done "on the fly." ESTATS can be used in dynamics runs

or in other sampling procedures that result in serial calls to the ENERGY

subroutine. The facility will collect data points at specified sampling

intervals along a collection run for a specified step length and calculate

the running statistics. An initial portion of the collection run may be skipped

(e.g. for eliminating the equilibration period from the statistics during

dynamics). Results may be written either to standard output or to a file.

The facility will, if requested, "variable-ize" the calculated averages, i.e.

allow assignment of the values to CHARMM script variables. The facility can

also write the individual potential energy values to a file.

Syntax:

ESTAts [LENGTH <integer>] [SKIP <integer>] [IPRF <integer>]

[NPRI <integer>] [IUNW <integer>] [NEPR <integer>]

[IUPE <integer>]

[UPLM <real>] [LOLM <real>] [FRPI] [VARI]

[BOND] [ANGLe] [UREY-Bradley] [DIHEdral] [IMPRoper]

[VDWaals] [ELECtrostatics] [HBONding] [USER]

[SBOUnd] [ASP]

LENGth length of trajectory (number of total energy calculations)

from which sampling is to take place (default 0).

SKIP specifies a length of energy data points (calls to ENERGY)

after which the data collection is to begin (default 0).

IPRFreq specifies the frequency with which data points will be

collected (i.e. every IPRFrequency energy calculations).

[BOND], [ANGLE], etc.

the energy term keywords specify which components of the potential

energy are to have their statistics calculated. HBONding is

the hydrogen bonding energy; USER is the user-defined energy;

SBOUnd is the solvent boundary potential; ASP is the implicit

solvation energy (e.g. from eef1). Statistics on the total

potential energy are always calculated.

IUNWrite fortran unit onto which statistics are to be written

(default is no printing)

NPRInt period for writing the energy statistics to standard output

(default is no printing)

IUPE fortran unit onto which the potential energies are to be

written (default is no printing)

NEPRint period for writing potential energies

UPLM limit above which an energy value will be discarded from the

statistics (default 99999999).

LOLM limit below which an energy value will be discarded from the

statistics (default -99999999).

FPRI keyword specifying the final statistics are to be written to

standard output at the end of the collection

STOP stops the data collection and prints current statistics

VARI keyword specifying that values of averages and variances will

be assignable to CHARMM script variables.

The values can be accessed as follows:

?AENE,?VENE mean and variance for potential energy

?ABON,?VBON mean and variance for bonds

?AANG,?VANG for angles

?AURE,?VURE for Urey-Bradley terms

?ADIH,?VDIH for dihedral terms

?AIMP,?VIMP for improper dihedral terms

?AVDW,?VVDW for van der Waals

?AELE,?VELE for electrostatics

?AHBO,?VHBO for hydrogen bond terms

?AUSE,?VUSE for user energy

?ASBO,?VSBO for solvent boundary potential (sbound)

?AASP,?VASP for solvation term

Note that ALL component energy terms for which statistics are being calculated

must be in the proper range (>LOLM and <UPLM) in order for a given data point

to be included. Discarded data points will result in statistics that are

based on less than LENGTH data points. The number of discarded data points

will be printed to standard output with the final statistics at the end of

the collection.

EXAMPLE:

ESTAts LENGTH 1000000 SKIP 100000 IPRFreq 5 NPRINT -1 FPRInt -

VDW ELEC BOND ANGL IMPR SBOU DIHE -

IUNWrite 11 NUPRint 10000 NEPR 1000 IUPE 10

This specifies that the statistics are to be done on 180,000 data points

(1,000,000 - 100,000)/5. Statistics will be done on the specified

energy terms in addition to the potential energy. Statistics will be

written every 10,000 steps to unit 11 and the potential energies

will be written every 1000 steps to unit 10. No printing will be

done to standard output (NPRINT -1) except for the final statistics

(FPRInt).

This statistics file is written out according to the following format:

EPOT 10 -1912.29336237 226.63620520

BOND 10 212.58550818 91.35922427

ANGL 10 299.99516787 95.65303762

UREY 10 39.09373234 18.64669506

The first column indicates the energy term.

The second column indicates the number of data points included in the

calculations (number of values over which statistics are taken).

The third column gives the average and the fourth column gives the

fluctuation (standard deviation).

(Differences between ESTATS and statistics calculated in standard

dynamics:

1) In ESTATS, the denominator in the standard deviation formula is

(N-1)^(1/2), where N is the number of data points. In dynamics,

the denominator is N^(1/2).

2) In dynamics, the initial energy terms are considered step "0" and

not included in the statistics; hence for a direct comparison, it

is necessary to specify SKIP 1 in the ESTATS command and increase

the LENGTH of the collection by 1.

Running Energy Averages (ESTATS)

The ESTATS command is a basic statistical facility that allows the

calculation and manipulation of the mean and variance of the potential

energy and its components over a number of potential energy calculations,

without the need for writing out trajectories or coordinate files--i.e.

the calculations are done "on the fly." ESTATS can be used in dynamics runs

or in other sampling procedures that result in serial calls to the ENERGY

subroutine. The facility will collect data points at specified sampling

intervals along a collection run for a specified step length and calculate

the running statistics. An initial portion of the collection run may be skipped

(e.g. for eliminating the equilibration period from the statistics during

dynamics). Results may be written either to standard output or to a file.

The facility will, if requested, "variable-ize" the calculated averages, i.e.

allow assignment of the values to CHARMM script variables. The facility can

also write the individual potential energy values to a file.

Syntax:

ESTAts [LENGTH <integer>] [SKIP <integer>] [IPRF <integer>]

[NPRI <integer>] [IUNW <integer>] [NEPR <integer>]

[IUPE <integer>]

[UPLM <real>] [LOLM <real>] [FRPI] [VARI]

[BOND] [ANGLe] [UREY-Bradley] [DIHEdral] [IMPRoper]

[VDWaals] [ELECtrostatics] [HBONding] [USER]

[SBOUnd] [ASP]

LENGth length of trajectory (number of total energy calculations)

from which sampling is to take place (default 0).

SKIP specifies a length of energy data points (calls to ENERGY)

after which the data collection is to begin (default 0).

IPRFreq specifies the frequency with which data points will be

collected (i.e. every IPRFrequency energy calculations).

[BOND], [ANGLE], etc.

the energy term keywords specify which components of the potential

energy are to have their statistics calculated. HBONding is

the hydrogen bonding energy; USER is the user-defined energy;

SBOUnd is the solvent boundary potential; ASP is the implicit

solvation energy (e.g. from eef1). Statistics on the total

potential energy are always calculated.

IUNWrite fortran unit onto which statistics are to be written

(default is no printing)

NPRInt period for writing the energy statistics to standard output

(default is no printing)

IUPE fortran unit onto which the potential energies are to be

written (default is no printing)

NEPRint period for writing potential energies

UPLM limit above which an energy value will be discarded from the

statistics (default 99999999).

LOLM limit below which an energy value will be discarded from the

statistics (default -99999999).

FPRI keyword specifying the final statistics are to be written to

standard output at the end of the collection

STOP stops the data collection and prints current statistics

VARI keyword specifying that values of averages and variances will

be assignable to CHARMM script variables.

The values can be accessed as follows:

?AENE,?VENE mean and variance for potential energy

?ABON,?VBON mean and variance for bonds

?AANG,?VANG for angles

?AURE,?VURE for Urey-Bradley terms

?ADIH,?VDIH for dihedral terms

?AIMP,?VIMP for improper dihedral terms

?AVDW,?VVDW for van der Waals

?AELE,?VELE for electrostatics

?AHBO,?VHBO for hydrogen bond terms

?AUSE,?VUSE for user energy

?ASBO,?VSBO for solvent boundary potential (sbound)

?AASP,?VASP for solvation term

Note that ALL component energy terms for which statistics are being calculated

must be in the proper range (>LOLM and <UPLM) in order for a given data point

to be included. Discarded data points will result in statistics that are

based on less than LENGTH data points. The number of discarded data points

will be printed to standard output with the final statistics at the end of

the collection.

EXAMPLE:

ESTAts LENGTH 1000000 SKIP 100000 IPRFreq 5 NPRINT -1 FPRInt -

VDW ELEC BOND ANGL IMPR SBOU DIHE -

IUNWrite 11 NUPRint 10000 NEPR 1000 IUPE 10

This specifies that the statistics are to be done on 180,000 data points

(1,000,000 - 100,000)/5. Statistics will be done on the specified

energy terms in addition to the potential energy. Statistics will be

written every 10,000 steps to unit 11 and the potential energies

will be written every 1000 steps to unit 10. No printing will be

done to standard output (NPRINT -1) except for the final statistics

(FPRInt).

This statistics file is written out according to the following format:

EPOT 10 -1912.29336237 226.63620520

BOND 10 212.58550818 91.35922427

ANGL 10 299.99516787 95.65303762

UREY 10 39.09373234 18.64669506

The first column indicates the energy term.

The second column indicates the number of data points included in the

calculations (number of values over which statistics are taken).

The third column gives the average and the fourth column gives the

fluctuation (standard deviation).

(Differences between ESTATS and statistics calculated in standard

dynamics:

1) In ESTATS, the denominator in the standard deviation formula is

(N-1)^(1/2), where N is the number of data points. In dynamics,

the denominator is N^(1/2).

2) In dynamics, the initial energy terms are considered step "0" and

not included in the statistics; hence for a direct comparison, it

is necessary to specify SKIP 1 in the ESTATS command and increase

the LENGTH of the collection by 1.

Top

Multiple Energy Evaluations for Related Conformations

The purpose of the MLTE command is to make repeated energy evaluations

for related conformations through rapid reading of pre-computed coordinates.

The MLTE command is invoked from the command line after a valid UPDAte

command has specified the energy function desired.

[SYNTAX MLTE]

MLTE [ ATNI atom_i ] [ ATNJ atom_j ] [ FILI filename_i ] [ FILJ filename_j ]

[ OUTF filename_output ]

repeat ( [ETER eterm] )

Cartesian coordinates for a collection of coordinates for two sets of atoms

are stored in "write coor dumb" format in files whose names are indicated by

FILI and FILJ, respectively. The number of the first atom of group_i is given

by ATNI and that of group_j is given by ATNJ. The energy for all

conformational pairings (each conformation of group_i with each conformation

of group_j) will be computed and printed in the file indicated by OUTF. The

energy terms to be included is indicated with repeated invocations of the

ETER command, with energy term names listed in the substitution section.

Multiple Energy Evaluations for Related Conformations

The purpose of the MLTE command is to make repeated energy evaluations

for related conformations through rapid reading of pre-computed coordinates.

The MLTE command is invoked from the command line after a valid UPDAte

command has specified the energy function desired.

[SYNTAX MLTE]

MLTE [ ATNI atom_i ] [ ATNJ atom_j ] [ FILI filename_i ] [ FILJ filename_j ]

[ OUTF filename_output ]

repeat ( [ETER eterm] )

Cartesian coordinates for a collection of coordinates for two sets of atoms

are stored in "write coor dumb" format in files whose names are indicated by

FILI and FILJ, respectively. The number of the first atom of group_i is given

by ATNI and that of group_j is given by ATNJ. The energy for all

conformational pairings (each conformation of group_i with each conformation

of group_j) will be computed and printed in the file indicated by OUTF. The

energy terms to be included is indicated with repeated invocations of the

ETER command, with energy term names listed in the substitution section.