Main Table of Contents

Thu 26 Aug 2010


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:
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.


-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]h gmx_bool no Print help info and quit
-[no]version gmx_bool no 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]w gmx_bool no View output xvg, xpm, eps and pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]sum gmx_bool no Sum the energy terms selected rather than display them all
-skip int 0 Skip number of frames between data points
-[no]mean gmx_bool 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]coul gmx_bool yes extract Coulomb SR energies
-[no]coulr gmx_bool no extract Coulomb LR energies
-[no]coul14 gmx_bool no extract Coulomb 1-4 energies
-[no]lj gmx_bool yes extract Lennard-Jones SR energies
-[no]lj gmx_bool no extract Lennard-Jones LR energies
-[no]lj14 gmx_bool no extract Lennard-Jones 1-4 energies
-[no]bhamsr gmx_bool no extract Buckingham SR energies
-[no]bhamlr gmx_bool no extract Buckingham LR energies
-[no]free gmx_bool yes calculate free energy
-temp real 300 reference temperature for free energy calculation