table of contents
g_spol(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_spol(1) |
NAME¶
g_spol - analyzes solvent dipole orientation and polarization around solutesSYNOPSIS¶
g_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]com -refat int -rmin real -rmax real -dip real -bw realDESCRIPTION¶
g_spol analyzes dipoles around a solute; it is especially useful for polarizable water. A group of reference atoms, or a center of mass reference (option -com) and a group of solvent atoms is required. The program splits the group of solvent atoms into molecules. For each solvent molecule the distance to the closest atom in reference group or to the COM is determined. A cumulative distribution of these distances is plotted. For each distance between -rmin and -rmax the inner product of the distance vector and the dipole of the solvent molecule is determined. For solvent molecules with net charge (ions), the net charge of the ion is subtracted evenly from all atoms in the selection of each ion. The average of these dipole components is printed. The same is done for the polarization, where the average dipole is subtracted from the instantaneous dipole. The magnitude of the average dipole is set with the option -dip, the direction is defined by the vector from the first atom in the selected solvent group to the midpoint between the second and the third atom.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Run input file: tpr tpb tpa
Index file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Use the center of mass as the reference postion
The reference atom of the solvent molecule
Maximum distance (nm)
Maximum distance (nm)
The average dipole (D)
The bin width
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |