gen_table_d (1) - Linux Manuals

gen_table_d: generate tables for use by mdrun

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)