g_enemat_d (1) - Linux Manuals

g_enemat_d: extracts an energy matrix from an energy file


g_enemat - extracts an energy matrix from an energy file



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


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: 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 


 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)

 View output xvg, xpm, eps and pdb files

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

 Sum the energy terms selected rather than display them all

-skip int 0
 Skip number of frames between data points

 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

 extract Coulomb SR energies

 extract Coulomb LR energies

 extract Coulomb 1-4 energies

 extract Lennard-Jones SR energies

 extract Lennard-Jones LR energies

 extract Lennard-Jones 1-4 energies

 extract Buckingham SR energies

 extract Buckingham LR energies

 calculate free energy

-temp real 300
 reference temperature for free energy calculation



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