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g_enemat_d

NAME

g_enemat - extracts an energy matrix from an energy file

SYNOPSIS

g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[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.
 Generic energy: edr ene 

-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]h no
 Print help 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]w no
 View output xvg, xpm, eps and pdb files

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[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 in stead 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]coul yes
 extract Coulomb SR energies

-[no]coulr no
 extract Coulomb LR energies

-[no]coul14 no
 extract Coulomb 1-4 energies

-[no]lj yes
 extract Lennard-Jones SR energies

-[no]lj 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 ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.