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gmx-enemat - Extract an energy matrix from an energy file


gmx enemat [-f [<.edr>]] [-groups [<.dat>]] [-eref [<.dat>]]
[-emat [<.xpm>]] [-etot [<.xvg>]] [-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>]


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:


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 to specify input files:

-f [<.edr>] (ener.edr) (Optional)
Energy file

-groups [<.dat>] (groups.dat)
Generic data file

-eref [<.dat>] (eref.dat) (Optional)
Generic data file

Options to specify output files:

-emat [<.xpm>] (emat.xpm)
X PixMap compatible matrix file

-etot [<.xvg>] (energy.xvg)
xvgr/xmgr file

Other options:

-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>
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

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