1 .TH g_spol 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_spol - analyzes solvent dipole orientation and polarization around solutes
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " scdist.xvg "
13 .BI "\-[no]version" ""
27 \&g_spol analyzes dipoles around a solute; it is especially useful
28 \&for polarizable water. A group of reference atoms, or a center
29 \&of mass reference (option \fB \-com\fR) and a group of solvent
30 \&atoms is required. The program splits the group of solvent atoms
31 \&into molecules. For each solvent molecule the distance to the
32 \&closest atom in reference group or to the COM is determined.
33 \&A cumulative distribution of these distances is plotted.
34 \&For each distance between \fB \-rmin\fR and \fB \-rmax\fR
35 \&the inner product of the distance vector
36 \&and the dipole of the solvent molecule is determined.
37 \&For solvent molecules with net charge (ions), the net charge of the ion
38 \&is subtracted evenly at all atoms in the selection of each ion.
39 \&The average of these dipole components is printed.
40 \&The same is done for the polarization, where the average dipole is
41 \&subtracted from the instantaneous dipole. The magnitude of the average
42 \&dipole is set with the option \fB \-dip\fR, the direction is defined
43 \&by the vector from the first atom in the selected solvent group
44 \&to the midpoint between the second and the third atom.
48 Trajectory: xtc trr trj gro g96 pdb cpt
50 .BI "\-s" " topol.tpr"
52 Run input file: tpr tpb tpa
54 .BI "\-n" " index.ndx"
58 .BI "\-o" " scdist.xvg"
64 Print help info and quit
66 .BI "\-[no]version" "no "
67 Print version info and quit
69 .BI "\-nice" " int" " 19"
72 .BI "\-b" " time" " 0 "
73 First frame (ps) to read from trajectory
75 .BI "\-e" " time" " 0 "
76 Last frame (ps) to read from trajectory
78 .BI "\-dt" " time" " 0 "
79 Only use frame when t MOD dt = first time (ps)
82 View output xvg, xpm, eps and pdb files
84 .BI "\-xvg" " enum" " xmgrace"
85 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
88 Use the center of mass as the reference postion
90 .BI "\-refat" " int" " 1"
91 The reference atom of the solvent molecule
93 .BI "\-rmin" " real" " 0 "
96 .BI "\-rmax" " real" " 0.32 "
99 .BI "\-dip" " real" " 0 "
100 The average dipole (D)
102 .BI "\-bw" " real" " 0.01 "
108 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.