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.TH "GMX-ENEMAT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
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.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
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.SH SYNOPSIS
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gmx enemat [\fB\-f\fP \fI[<.edr>]\fP] [\fB\-groups\fP \fI[<.dat>]\fP] [\fB\-eref\fP \fI[<.dat>]\fP]
           [\fB\-emat\fP \fI[<.xpm>]\fP] [\fB\-etot\fP \fI[<.xvg>]\fP] [\fB\-b\fP \fI<time>\fP] [\fB\-e\fP \fI<time>\fP]
           [\fB\-dt\fP \fI<time>\fP] [\fB\-[no]w\fP] [\fB\-xvg\fP \fI<enum>\fP] [\fB\-[no]sum\fP]
           [\fB\-skip\fP \fI<int>\fP] [\fB\-[no]mean\fP] [\fB\-nlevels\fP \fI<int>\fP] [\fB\-max\fP \fI<real>\fP]
           [\fB\-min\fP \fI<real>\fP] [\fB\-[no]coulsr\fP] [\fB\-[no]coul14\fP] [\fB\-[no]ljsr\fP]
           [\fB\-[no]lj14\fP] [\fB\-[no]bhamsr\fP] [\fB\-[no]free\fP] [\fB\-temp\fP \fI<real>\fP]
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.fi
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.SH DESCRIPTION
.sp
\fBgmx enemat\fP extracts an energy matrix from the energy file (\fB\-f\fP).
With \fB\-groups\fP 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 \fB\-groups\fP file contains:
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Protein
SOL
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then energy groups with names like ‘Coul\-SR:Protein\-SOL’ and
‘LJ:Protein\-SOL’ are expected in the energy file (although
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\fBgmx enemat\fP is most useful if many groups are analyzed
simultaneously). Matrices for different energy types are written
out separately, as controlled by the
\fB\-[no]coul\fP, \fB\-[no]coulr\fP, \fB\-[no]coul14\fP,
\fB\-[no]lj\fP, \fB\-[no]lj14\fP,
\fB\-[no]bham\fP and \fB\-[no]free\fP options.
Finally, the total interaction energy energy per group can be
calculated (\fB\-etot\fP).
.sp
An approximation of the free energy can be calculated using:
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E_free = E_0 + kT log(<exp((E\-E_0)/kT)>), where ‘<>’
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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 \fB\-groups\fP file, but a appended number
(e.g. residue number) in the \fB\-groups\fP will be ignored
in the comparison.
.SH OPTIONS
.sp
Options to specify input files:
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.B \fB\-f\fP [<.edr>] (ener.edr) (Optional)
Energy file
.TP
.B \fB\-groups\fP [<.dat>] (groups.dat)
Generic data file
.TP
.B \fB\-eref\fP [<.dat>] (eref.dat) (Optional)
Generic data file
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Options to specify output files:
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.B \fB\-emat\fP [<.xpm>] (emat.xpm)
X PixMap compatible matrix file
.TP
.B \fB\-etot\fP [<.xvg>] (energy.xvg)
xvgr/xmgr file
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Other options:
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.B \fB\-b\fP <time> (0)
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Time of first frame to read from trajectory (default unit ps)
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.TP
.B \fB\-e\fP <time> (0)
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Time of last frame to read from trajectory (default unit ps)
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.TP
.B \fB\-dt\fP <time> (0)
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Only use frame when t MOD dt = first time (default unit ps)
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.TP
.B \fB\-[no]w\fP  (no)
View output \&.xvg, \&.xpm, \&.eps and \&.pdb files
.TP
.B \fB\-xvg\fP <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
.TP
.B \fB\-[no]sum\fP  (no)
Sum the energy terms selected rather than display them all
.TP
.B \fB\-skip\fP <int> (0)
Skip number of frames between data points
.TP
.B \fB\-[no]mean\fP  (yes)
with \fB\-groups\fP extracts matrix of mean energies instead of matrix for each timestep
.TP
.B \fB\-nlevels\fP <int> (20)
number of levels for matrix colors
.TP
.B \fB\-max\fP <real> (1e+20)
max value for energies
.TP
.B \fB\-min\fP <real> (\-1e+20)
min value for energies
.TP
.B \fB\-[no]coulsr\fP  (yes)
extract Coulomb SR energies
.TP
.B \fB\-[no]coul14\fP  (no)
extract Coulomb 1\-4 energies
.TP
.B \fB\-[no]ljsr\fP  (yes)
extract Lennard\-Jones SR energies
.TP
.B \fB\-[no]lj14\fP  (no)
extract Lennard\-Jones 1\-4 energies
.TP
.B \fB\-[no]bhamsr\fP  (no)
extract Buckingham SR energies
.TP
.B \fB\-[no]free\fP  (yes)
calculate free energy
.TP
.B \fB\-temp\fP <real> (300)
reference temperature for free energy calculation
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.SH SEE ALSO
.sp
\fBgmx(1)\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
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2018, GROMACS development team
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