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g_potential
Langue: en
Version: 370142 (fedora - 01/12/10)
Section: 1 (Commandes utilisateur)
NAME
g_potential - calculates the electrostatic potential across the boxVERSION 4.5
SYNOPSIS
g_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correctDESCRIPTION
Compute the electrostatical potential across the box. The potential is calculated by first summing the charges per slice and then integrating twice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side of the box. It's also possible to calculate the potential in spherical coordinates as function of r by calculating a charge distribution in spherical slices and twice integrating them. epsilon_r is taken as 1, 2 is more appropriate in many cases.FILES
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-o potential.xvg Output
xvgr/xmgr file
-oc charge.xvg Output
xvgr/xmgr file
-of field.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hnoPrint help info and quit
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-d string Z
Take the normal on the membrane in direction X, Y or Z.
-sl int 10
Calculate potential as function of boxlength, dividing the box in nr slices.
-cb int 0
Discard first nr slices of box for integration
-ce int 0
Discard last nr slices of box for integration
-tz real 0
Translate all coordinates distance in the direction of the box
-[no]sphericalno
Calculate spherical thingie
-ng int 1
Number of groups to consider
-[no]correctno
Assume net zero charge of groups to improve accuracy
KNOWN PROBLEMS
- Discarding slices for integration should not be necessary.SEE ALSO
gromacs(7)More information about GROMACS is available at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre