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Power & Cooling - Harness energy like a resource
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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 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/>. Mon 4 Apr 2011 g_enemat(1)
