[gmx-users] g_dipoles -slab option
Bob Johnson
robertjo at physics.upenn.edu
Thu May 25 02:37:01 CEST 2006
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
More information about the gromacs.org_gmx-users
mailing list