NAME¶

g_enemat - extracts an energy matrix from an energy file VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[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.
Energy file -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]hno
Print help info and quit -[no]versionno
Print version 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]wno
View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -[no]sumno
Sum the energy terms selected rather than display them all -skip int 0
Skip number of frames between data points -[no]meanyes
with -groups extracts matrix of mean energies instead 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]coulyes
extract Coulomb SR energies -[no]coulrno
extract Coulomb LR energies -[no]coul14no
extract Coulomb 1-4 energies -[no]ljyes
extract Lennard-Jones SR energies -[no]ljno
extract Lennard-Jones LR energies -[no]lj14no
extract Lennard-Jones 1-4 energies -[no]bhamsrno
extract Buckingham SR energies -[no]bhamlrno
extract Buckingham LR energies -[no]freeyes
calculate free energy -temp real 300
reference temperature for free energy calculation

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.