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.
* Menu:
* 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
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. See *note Minimiz:(chmdoc/minimiz.do,,) and
*note Gete:(usage.doc)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 ] [ COMP ]
[ INBFrq 0 ] [ IHBFrq 0 ] [ IMGFrq 0 ] [NOUPdate]
hbond-spec *note Hbonds:(hbonds.doc).
nonbond-spec *note Nbonds:(nbonds.doc).
image-spec *note Images:(images.doc)Update.
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 ] ]
[ 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).
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 ]
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
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
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
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.
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.
[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
VECTor 3
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)
FASTer 3 : Use fast vector 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]
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, see *note Hbond: (hbonds.doc), must be
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
*note read:(io.doc)read, or generate them with separate
commands, see *note HBgen:(hbonds.doc), or
*note NBgen:(nbonds.doc).
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, see *note Cons:(cons.doc), can
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, see *note shake:(cons.doc)SHAKE, is
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. See *note Modify:(usage.doc)interface for details.
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
'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
*
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.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute