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Langue: en

Version: 369779 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)


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 -[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


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 


 Print help info and quit

 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)

 View output xvg, xpm, eps and pdb files

-xvg enum xmgrace
 xvg plot formatting:  xmgrace xmgr or  none

 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 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

 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



More information about GROMACS is available at <>.

02:40 Comment va-t-on faire pour la couverture GSM dans les zones
accidentées ? Où faudra-t-il aller pour vivre dans un environnement
électromagnétiquement sain ?
08:18 et enfouillir les relais, ils y ont pensé à enfouillir ces relais
tout moche qui gâche le paysage ????