Main Table of Contents

Fri 5 Jul 2013


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 = E_0 + kT log(), 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 bool no Print help info and quit
-[no]version 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 bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]sum bool no Sum the energy terms selected rather than display them all
-skip int 0 Skip number of frames between data points
-[no]mean 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]coulsr bool yes extract Coulomb SR energies
-[no]coullr bool no extract Coulomb LR energies
-[no]coul14 bool no extract Coulomb 1-4 energies
-[no]ljsr bool yes extract Lennard-Jones SR energies
-[no]ljlr bool no extract Lennard-Jones LR energies
-[no]lj14 bool no extract Lennard-Jones 1-4 energies
-[no]bhamsr bool no extract Buckingham SR energies
-[no]bhamlr bool no extract Buckingham LR energies
-[no]free bool yes calculate free energy
-temp real 300 reference temperature for free energy calculation