g_enemat(1)
NAME
g_enemat - extracts an energy matrix from an energy file
SYNOPSIS
g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]sum -skip int -[no]mean -nlevels int -max real -min real -[no]coul -[no]coulr -[no]coul14 -[no]lj -[no]lj -[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free -temp real
DESCRIPTION
g_enemat extracts an energy matrix from the energy file ( -f ). With
-groups a file must be supplied with on each line a group of atoms to
be used. For these groups matrix of interaction energies will be
extracted from the energy file by looking for energy groups with names
corresponding to pairs of groups of atoms. E.g. if your -groups file
contains:
2
Protein
SOL
then energy groups with names like 'Coul-SR:Protein-SOL' and 'LJ:Protein-SOL' are expected in the energy file (although
g_enemat is most useful if many groups are analyzed simultaneously).
Matrices for different energy types are written out separately, as controlled by the
-[no]coul , -[no]coulr , -[no]coul14 ,
-[no]lj , -[no]lj14 ,
-[no]bham and -[no]free options. Finally, the total interaction energy
energy per group can be calculated ( -etot ).
An approximation of the free energy can be calculated using: E(free) =
E0 + kT log( exp((E-E0)/kT) ), where '' stands for time-average. A file
with reference free energies can be supplied to calculate the free
energy difference with some reference state. Group names (e.g. residue
names) in the reference file should correspond to the group names as
used in the -groups file, but a appended number (e.g. residue number)
in the -groups will be ignored in the comparison.
FILES
- -f ener.edr Input, Opt.
- Generic energy: edr ene
- -groups groups.dat Input
- Generic data file
- -eref eref.dat Input, Opt.
- Generic data file
- -emat emat.xpm Output
- X PixMap compatible matrix file
- -etot energy.xvg Output
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 19
- Set the nicelevel
- -b time 0
- First frame (ps) to read from trajectory
- -e time 0
- Last frame (ps) to read from trajectory
- -dt time 0
- Only use frame when t MOD dt = first time (ps)
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -[no]sum no
- Sum the energy terms selected rather than display them all
- -skip int 0
- Skip number of frames between data points
- -[no]mean yes
- with -groups extracts matrix of mean energies in stead of matrix for
- each timestep
- -nlevels int 20
- number of levels for matrix colors
- -max real 1e+20
- max value for energies
- -min real -1e+20
- min value for energies
- -[no]coul yes
- extract Coulomb SR energies
- -[no]coulr no
- extract Coulomb LR energies
- -[no]coul14 no
- extract Coulomb 1-4 energies
- -[no]lj yes
- extract Lennard-Jones SR energies
- -[no]lj no
- extract Lennard-Jones LR energies
- -[no]lj14 no
- extract Lennard-Jones 1-4 energies
- -[no]bhamsr no
- extract Buckingham SR energies
- -[no]bhamlr no
- extract Buckingham LR energies
- -[no]free yes
- calculate free energy
- -temp real 300
- reference temperature for free energy calculation
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.