gen_table(1)
NAME
gen_table - generate tables for use by mdrun
VERSION 4.0_rc1
SYNOPSIS
gen_table -o table.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -el enum -rc real -rtol real -xi real -xir real -z1 real -z2 real -nrow1 int -nrow2 int -m enum -resol int -delta real -efac real -nrep int -ndisp int
DESCRIPTION
gen_table generates tables for mdrun for use with the USER defined
potentials. Note that the format has been update for higher accuracy in
the forces starting with version 4.0. Using older tables with 4.0 will
silently crash your simulations, as will using new tables with an older
GROMACS version. This is because in the old version the second derevative of the potential was specified whereas in the new version the
first derivative of the potential is used instead.
For Slater interactions four parameters must be passed: the 1/Width and
the row number of the element. The interactions are computed analytically which may be slow due to the fact that arbitraray precision
arithmetic is needed. If the width of one of the Slater is zero a
Nucleus-Slater interaction will be generated.
FILES
- -o table.xvg Output
- xvgr/xmgr file
OTHER OPTIONS
- -[no]hno
- 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]wno
- View output xvg, xpm, eps and pdb files
- -[no]xvgryes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -el enum cut
- Electrostatics type: cut, rf or pme: cut , rf or pme
- -rc real 0.9
- Cut-off required for rf or pme
- -rtol real 1e-05
- Ewald tolerance required for pme
- -xi real 0.15
- Width of the Gaussian diffuse charge of the G&G model
- -xir real 0.0615
- Width of erfc(z)/z repulsion of the G&G model (z=0.5 rOO/xir)
- -z1 real 20
- 1/Width of the first Slater charge (unit 1/nm)
- -z2 real 20
- 1/Width of the second Slater charge (unit 1/nm)
- -nrow1 int 1
- Row number for the first Slater charge
- -nrow2 int 1
- Row number for the first Slater charge
- -m enum ljc
- Model for the tables: ljc , gg , guillot2001a or slater
- -resol int 500
- Resolution of the table (points per nm)
- -delta real 0
- Displacement in the Coulomb functions (nm), used as 1/(r+delta). Only
- for hard wall potential.
- -efac real 500
- Number indicating the steepness of the hardwall potential.
- -nrep int 12
- Power for the repulsion potential (with model AB1 or maaren)
- -ndisp int 6
- Power for the dispersion potential (with model AB1 or maaren)