table of contents
g_enemat(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_enemat(1) |
NAME¶
g_enemat - extracts an energy matrix from an energy fileSYNOPSIS¶
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 realDESCRIPTION¶
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:FILES¶
-f ener.edr Input, Opt.Energy file
Generic data file
Generic data file
X PixMap compatible matrix file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Sum the energy terms selected rather than display them all
Skip number of frames between data points
with -groups extracts matrix of mean energies instead of matrix for each timestep
number of levels for matrix colors
max value for energies
min value for energies
extract Coulomb SR energies
extract Coulomb LR energies
extract Coulomb 1-4 energies
extract Lennard-Jones SR energies
extract Lennard-Jones LR energies
extract Lennard-Jones 1-4 energies
extract Buckingham SR energies
extract Buckingham LR energies
calculate free energy
reference temperature for free energy calculation
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |