Visit The New, Modern Unix Linux Community

Linux and UNIX Man Pages

Test Your Knowledge in Computers #637
Difficulty: Easy
As of January 2017, Apple's App Store had over 2.2 million apps for the iPhone.
True or False?
Linux & Unix Commands - Search Man Pages

g_sorient(1) [debian man page]

g_sorient(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_sorient(1)

NAME
g_sorient - analyzes solvent orientation around solutes VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc DESCRIPTION
g_sorient analyzes solvent orientation around solutes. It calculates two angles between the vector from one or more reference positions to the first atom of each solvent molecule: theta1: the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3. theta2: the angle with the normal of the solvent plane, defined by the same three atoms, or, when the option -v23 is set, the angle with the vector between atoms 2 and 3. The reference can be a set of atoms or the center of mass of a set of atoms. The group of solvent atoms should consist of 3 atoms per sol- vent molecule. Only solvent molecules between -rmin and -rmax are considered for -o and -no each frame. -o: distribtion of cos(theta1) for rmin=r=rmax. -no: distribution of cos(theta2) for rmin=r=rmax. -ro: cos(theta1) and 3cos2(theta2)-1 as a function of the distance. -co: the sum over all solvent molecules within distance r of cos(theta1) and 3cos2(theta2)-1 as a function of r. -rc: the distribution of the solvent molecules as a function of r FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -o sori.xvg Output xvgr/xmgr file -no snor.xvg Output xvgr/xmgr file -ro sord.xvg Output xvgr/xmgr file -co scum.xvg Output xvgr/xmgr file -rc scount.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 -[no]comno Use the center of mass as the reference postion -[no]v23no Use the vector between atoms 2 and 3 -rmin real 0 Minimum distance (nm) -rmax real 0.5 Maximum distance (nm) -cbin real 0.02 Binwidth for the cosine -rbin real 0.02 Binwidth for r (nm) -[no]pbcno Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_sorient(1)

Check Out this Related Man Page

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)

Featured Tech Videos