g_potential(1) [debian man page]
g_potential(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_potential(1) NAME
g_potential - calculates the electrostatic potential across the box VERSION 4.5.4-dev-20110404-bc5695c 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]correct DESCRIPTION
g_potential computes 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 is 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, but 2 is more appropriate in many cases. FILES
-f traj.xtc Input Trajectory: 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]hno Print 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/>. Mon 4 Apr 2011 g_potential(1)
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g_sgangle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sgangle(1) NAME
g_sgangle - computes the angle and distance between two groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]one -[no]z DESCRIPTION
Compute the angle and distance between two groups. The groups are defined by a number of atoms given in an index file and may be two or three atoms in size. If -one is set, only one group should be specified in the index file and the angle between this group at time 0 and t will be computed. The angles calculated depend on the order in which the atoms are given. Giving, for instance, 5 6 will rotate the vec- tor 5-6 with 180 degrees compared to giving 6 5. If three atoms are given, the normal on the plane spanned by those three atoms will be calculated, using the formula P1P2 x P1P3. The cos of the angle is calculated, using the inproduct of the two normalized vectors. Here is what some of the file options do: -oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used. -od: Distance between two groups. Distance is taken from the center of one group to the center of the other group. -od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately. -od2: For two planes this option has no meaning. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input Run input file: tpr tpb tpa -oa sg_angle.xvg Output xvgr/xmgr file -od sg_dist.xvg Output, Opt. xvgr/xmgr file -od1 sg_dist1.xvg Output, Opt. xvgr/xmgr file -od2 sg_dist2.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print 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 -[no]oneno Only one group compute angle between vector at time zero and time t -[no]zno Use the z-axis as reference SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_sgangle(1)