[gmx-users] Mass fraction

Steven Neumann s.neumann08 at gmail.com
Thu Feb 2 14:51:42 CET 2012

Dear Gmx Users,

My system consists of Protein attached to the surface (water solution)
I am trying to calculate equilibrium distance - dependent (from my
surface) distributions of residues (e.g. polar) in my system collected in
the mass fraction. So in this case I am interested in only one coordinate
(X) which perpendicular to my surface. I assume to use just last 5-10 ns
(out of 100ns) as an equilibrium.

Is there any way to use g_rdf for this purpose?

Or shall I use g_dist, calculate distances of each residue (e.g. from polar
residues) for last 5-10 ns, take X coordinate, average it over time and
multiply by its mass?

Do you have any suggestions?

Thank you,

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