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)
Thu 16 Oct 2008 gen_table(1)