[gmx-users] g_dipoles -slab option

[Bob Johnson]

Hello everyone,
Water tends to align at a hydrophobic surface in a way to maximize H-bonds.
Doing this leads to a dipole moment that is perpendicular to the surface
(pointing away from the surface). Is this correct?

I'm trying to verify this with a simulation. I have an uncharged surface in the
xz-plane. I'm using g_dipoles with the -slab option to get the dipole moment of
water slabs in the y direction. Below is the output. There are 5 columns of data
for some reason and I can't interepret it. The first column is the position of
the water slab. I can only assume that column 2 is the dipole in the x
direction and column 3 is the dipole in the y direction and so on. Is that
correct? What is the last column for?


@    title "Average dipole moment per slab"
@    xaxis  label "Box-Y (nm)"
@    yaxis  label "\f{12}m\f{4} (D)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "\f{12}m\f{4}\sX\N"
@ s1 legend "\f{12}m\f{4}\sY\N"
@ s2 legend "\f{12}m\f{4}\sZ\N"
     0.500       0.000       0.000       0.000       0.000
     1.500     -46.367       3.869      41.074      62.064
     2.500      36.106       0.765       3.870      36.321
     3.500       7.638       0.371       1.223       7.744
     4.500     -18.688       1.380     -20.000      27.406
     5.500       8.237       4.201      -9.015      12.914
     6.500      -0.103       0.057      -0.023       0.119
     7.500       0.000       0.000       0.000       0.000
     8.500       0.000       0.000       0.000       0.000
     9.500       0.000       0.000       0.000       0.000


Thanks,
Bob Johnson