1GMX-SPOL(1)                         GROMACS                        GMX-SPOL(1)
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NAME

6       gmx-spol  -  Analyze solvent dipole orientation and polarization around
7       solutes
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SYNOPSIS

10          gmx spol [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
11                   [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
12                   [-xvg <enum>] [-[no]com] [-refat <int>] [-rmin <real>]
13                   [-rmax <real>] [-dip <real>] [-bw <real>]
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DESCRIPTION

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

34       Options to specify input files:
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36       -f [<.xtc/.trr/…>] (traj.xtc)
37              Trajectory: xtc trr cpt gro g96 pdb tng
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39       -s [<.tpr>] (topol.tpr)
40              Portable xdr run input file
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42       -n [<.ndx>] (index.ndx) (Optional)
43              Index file
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45       Options to specify output files:
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47       -o [<.xvg>] (scdist.xvg)
48              xvgr/xmgr file
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50       Other options:
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52       -b <time> (0)
53              Time of first frame to read from trajectory (default unit ps)
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55       -e <time> (0)
56              Time of last frame to read from trajectory (default unit ps)
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58       -dt <time> (0)
59              Only use frame when t MOD dt = first time (default unit ps)
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61       -[no]w (no)
62              View output .xvg, .xpm, .eps and .pdb files
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64       -xvg <enum> (xmgrace)
65              xvg plot formatting: xmgrace, xmgr, none
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67       -[no]com (no)
68              Use the center of mass as the reference position
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70       -refat <int> (1)
71              The reference atom of the solvent molecule
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73       -rmin <real> (0)
74              Maximum distance (nm)
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76       -rmax <real> (0.32)
77              Maximum distance (nm)
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79       -dip <real> (0)
80              The average dipole (D)
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82       -bw <real> (0.01)
83              The bin width
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SEE ALSO

86       gmx(1)
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88       More     information    about    GROMACS    is    available    at    <‐
89       http://www.gromacs.org/>.
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92       2019, GROMACS development team
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972019.2                           Apr 16, 2019                      GMX-SPOL(1)
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