gmx-enemat(1) GROMACS Manual gmx-enemat(1)NAMEgmx-enemat - Extract an energy matrix from an energy file
SYNOPSIS
gmx enemat [-f [<.edr>]] [-groups [<.dat>]] [-eref [<.dat>]]
[-emat [<.xpm>]] [-etot [<.xvg>]] [-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]coulsr]
[-[no]coullr] [-[no]coul14] [-[no]ljsr] [-[no]ljlr]
[-[no]lj14] [-[no]bhamsr] [-[no]bhamlr] [-[no]free]
[-temp <real>]
DESCRIPTION
gmx 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 gmx 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 =
E_0 + kT log(exp((E-E_0)/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.
OPTIONS
Options to specify input and output files:
-f [<.edr>] (ener.edr) (Input, Optional)
Energy file
-groups [<.dat>] (groups.dat) (Input)
Generic data file
-eref [<.dat>] (eref.dat) (Input, Optional)
Generic data file
-emat [<.xpm>] (emat.xpm) (Output)
X PixMap compatible matrix file
-etot [<.xvg>] (energy.xvg) (Output)
xvgr/xmgr file
Other options:
-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[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 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]coulsr (yes)
extract Coulomb SR energies
-[no]coullr (no)
extract Coulomb LR energies
-[no]coul14 (no)
extract Coulomb 1-4 energies
-[no]ljsr (yes)
extract Lennard-Jones SR energies
-[no]ljlr (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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-enemat(1)
