gmx spol#


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


gmx 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.


Options to specify input files:

-f [<.xtc/.trr/…>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr>] (topol.tpr)

Portable xdr run input file

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-o [<.xvg>] (scdist.xvg)

xvgr/xmgr file

Other options:

-b <time> (0)

Time of first frame to read from trajectory (default unit ps)

-e <time> (0)

Time of last frame to read from trajectory (default unit ps)

-dt <time> (0)

Only use frame when t MOD dt = first time (default unit ps)

-[no]w (no)

View output .xvg, .xpm, .eps and .pdb files

-xvg <enum> (xmgrace)

xvg plot formatting: xmgrace, xmgr, none

-[no]com (no)

Use the center of mass as the reference position

-refat <int> (1)

The reference atom of the solvent molecule

-rmin <real> (0)

Maximum distance (nm)

-rmax <real> (0.32)

Maximum distance (nm)

-dip <real> (0)

The average dipole (D)

-bw <real> (0.01)

The bin width