[gmx-users] Mass fraction

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 2 23:53:15 CET 2012

On 3/02/2012 12:51 AM, Steven Neumann 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?

This seems fine.


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