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g_enematMain Table of Contents |
VERSION 3.3_beta_20050823
Mon 29 Aug 2005
| VERSION 3.3_beta_20050823 |
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.
| option | filename | type | description |
|---|---|---|---|
| -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 |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | 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 | bool | no | View output xvg, xpm, eps and pdb files |
| -[no]xvgr | bool | yes | Add specific codes (legends etc.) in the output xvg files for the xmgrace program |
| -[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 in stead of matrix for each timestep |
| -nlevels | int | 20 | number of levels for matrix colors |
| -m ogram | |||
| -[no]com | bool | no | Plot data for the com of each group |
| -[no]mol | bool | no | Index contains molecule numbers iso atom numbers |
| -[no]nojump | bool | no | Remove jumps of atoms across the box |
| -[no]x | bool | yes | Plot X-component |
| -[no]y | bool | yes | Plot Y-component |
| -[no]z | bool | yes | Plot Z-component |
| -ng | int | 1 | Number of groups to consider |
| -[no]len | bool | no | Plot vector length |
| -bin | real | 1 | Binwidth for velocity histogram (nm/ps) |
| -scale | real | 0 | Scale factor for pdb output, 0 is autoscale |