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ffscanMain Table of Contents |
VERSION 3.3.1
Thu 11 May 2006
| VERSION 3.3.1 |
The ffscan program performs a single point energy and force calculation in which the force field is modified. This way a range of parameters can be changed and tested for reproduction of e.g. quantum chemical or experimental data. A grid scan over the parameters is done as specified using command line arguments. All parameters that reproduce the energy within a given absolute tolerance are printed to a log file.
Obviously polarizable models can be used, and shell optimisation is performed if necessary. Also, like in mdrun table functions can be used for user defined potential functions.
If the option -ga with appropriate file is passed, a genetic algorithm will be used rather than a grid scan.
| option | filename | type | description |
|---|---|---|---|
| -s | topol.tpr | Input | Generic run input: tpr tpb tpa xml |
| -g | md.log | Output | Log file |
| -table | table.xvg | Input, Opt. | xvgr/xmgr file |
| -parm | params.dat | Input | Generic data file |
| -ga | genalg.dat | Input, Opt. | Generic data file |
| -c | junk.gro | Output | Coordinate file in Gromos-87 format |
| -e | junk.edr | Output | Generic energy: edr ene |
| -o | junk.trr | Output | Full precision trajectory: trr trj |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 19 | Set the nicelevel |
| -[no]xvgr | bool | yes | Add specific codes (legends etc.) in the output xvg files for the xmgrace program |
| -tol | real | 0.1 | Energy tolerance (kJ/mol) (zero means everything is printed) |
| -fmax | real | 100 | Force tolerance (zero means everything is printed) |
| -[no]comb | bool | yes | Use combination rules |
| -npow | real | 12 | Power for LJ in case of table use |
| -[no]logeps | bool | no | Use a logarithmic scale for epsilon |
| -[no]v | bool | no | Be loud and noisy |
| -epot | real | 0 | Target energy (kJ/mol) |
| -fepot | real | 1 | Factor for scaling energy violations (0 turns energy contribution off) |
| -pres | real | 1 | Value for reference pressure |
| -fpres | real | 0.1 | Factor for scaling pressure violations (0 turns pressure contribution off) |
| -fmsf | real | 0.1 | Factor for scaling mean square force violations (0 turns MSF contribution off) |
| -molsize | int | 1 | Number of atoms per molecule |
| -nmol | int | 1 | Number of molecules (Epot is divided by this value!) |