[gmx-users] Re: Mass fraction

Steven Neumann s.neumann08 at gmail.com
Thu Feb 2 17:22:34 CET 2012

Anyone can help? Please...

On Thu, Feb 2, 2012 at 1:51 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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,
> Steven
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