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g_enematMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
g_enemat extracts an energy matrix from an energy file. With -groups a file must be supplied with on each line a group to be used. For these groups a matrices of interaction energies will be calculated. Also the total interaction energy energy per group is calculated.
An approximation of the free energy is 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 |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -nice | int | 19 | Set the nicelevel |
| -b | time | -1 | First frame (ps) to read from trajectory |
| -e | time | -1 | Last frame (ps) to read from trajectory |
| -dt | time | -1 | Only use frame when t MOD dt = first time (ps) |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -[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 calculates 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 |
| -[no]coul | bool | yes | calculate Coulomb SR energies |
| -[no]coulr | bool | no | calculate Coulomb LR energies |
| -[no]coul14 | bool | no | calculate Coulomb 1-4 energies |
| -[no]lj | bool | yes | calculate Lennard-Jones SR energies |
| -[no]lj14 | bool | no | calculate Lennard-Jones 1-4 energies |
| -[no]bham | bool | no | calculate Buckingham energies |
| -[no]free | bool | yes | calculate free energy |
| -temp | real | 300 | reference temperature for free energy calculation |