On Sat, Feb 28, 2015 at 11:39 AM, Robin Jain <robinjain.chem.gmail.com>
wrote:
> Dear all users,
> I have simulated a organic solute in water and i run a production run for
> 60ns.Now i want to analyze the spatial distribution function for water
> around organic solute. therefore i want your help that how can i analyze it
> from amber trajecotries . Please help me in this regard in brief.
>
​Look at the "grid" and "volmap" commands in cpptraj (they are described in
the manual). These will give you particle densities on a grid. If you
center and image your organic molecule, and it is rigid enough, you should
be able to get water densities around the molecule.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Feb 28 2015 - 13:30:02 PST
