1g_spol(1)                 GROMACS suite, VERSION 4.5                 g_spol(1)
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NAME

6       g_spol  -  analyzes  solvent dipole orientation and polarization around
7       solutes
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9       VERSION 4.5
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SYNOPSIS

12       g_spol -f traj.xtc -s  topol.tpr  -n  index.ndx  -o  scdist.xvg  -[no]h
13       -[no]version  -nice  int  -b  time  -e  time  -dt time -[no]w -xvg enum
14       -[no]com -refat int -rmin real -rmax real -dip real -bw real
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DESCRIPTION

17       g_spol analyzes dipoles around a solute; it is  especially  useful  for
18       polarizable water. A group of reference atoms, or a center of mass ref‐
19       erence (option  -com) and a group of solvent  atoms  is  required.  The
20       program splits the group of solvent atoms into molecules. For each sol‐
21       vent molecule the distance to the closest atom in reference group or to
22       the COM is determined.  A cumulative distribution of these distances is
23       plotted.  For each distance between  -rmin and  -rmax the inner product
24       of the distance vector and the dipole of the solvent molecule is deter‐
25       mined.  For solvent molecules with net charge (ions), the net charge of
26       the ion is subtracted evenly at all atoms in the selection of each ion.
27       The average of these dipole components is printed.  The  same  is  done
28       for  the  polarization, where the average dipole is subtracted from the
29       instantaneous dipole. The magnitude of the average dipole is  set  with
30       the option  -dip, the direction is defined by the vector from the first
31       atom in the selected solvent group to the midpoint between  the  second
32       and the third atom.
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FILES

35       -f traj.xtc Input
36        Trajectory: xtc trr trj gro g96 pdb cpt
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38       -s topol.tpr Input
39        Run input file: tpr tpb tpa
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41       -n index.ndx Input, Opt.
42        Index file
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44       -o scdist.xvg Output
45        xvgr/xmgr file
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OTHER OPTIONS

49       -[no]hno
50        Print help info and quit
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52       -[no]versionno
53        Print version info and quit
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55       -nice int 19
56        Set the nicelevel
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58       -b time 0
59        First frame (ps) to read from trajectory
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61       -e time 0
62        Last frame (ps) to read from trajectory
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64       -dt time 0
65        Only use frame when t MOD dt = first time (ps)
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67       -[no]wno
68        View output xvg, xpm, eps and pdb files
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70       -xvg enum xmgrace
71        xvg plot formatting:  xmgrace,  xmgr or  none
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73       -[no]comno
74        Use the center of mass as the reference postion
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76       -refat int 1
77        The reference atom of the solvent molecule
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79       -rmin real 0
80        Maximum distance (nm)
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82       -rmax real 0.32
83        Maximum distance (nm)
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85       -dip real 0
86        The average dipole (D)
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88       -bw real 0.01
89        The bin width
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SEE ALSO

93       gromacs(7)
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95       More   information  about  GROMACS  is  available  at  <http://www.gro‐
96       macs.org/>.
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100                                Thu 26 Aug 2010                      g_spol(1)
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