Re: [AMBER] RDF Plot

From: Jason Swails <>
Date: Wed, 04 Jun 2014 12:08:42 -0400

On Wed, 2014-06-04 at 08:04 -0700, zahra khatti wrote:
> Dear Amberists
> when I investigate my hydrophilic drug solvation in nanotube by
> atom-atom RDF, as well as for nanotube solvation.
> I get incorrect plot. My input file for running ptraj is as follow:
> trajin .mdcrd
> radial out-rdf.dat 0.1 30.0 :WAT.O :LIG.N1 closest
> attachment file is one of the plots.
> could you help me to solve the problem?

It is highly unlikely that your plot is incorrect. The mistake is
either what you assumed the RDF would look like or the masks you chose
to analyze (both issues depend on your particular system, so there is
limited technical help we can provide).

Your plot suggests to me that the local water-oxygen density around your
N1 atoms is lower than bulk density, with 3 solvation shells. You can
compute the RDF another way (like with VMD) to compare if you are
skeptical. You just have to make sure that periodic images are properly
accounted for.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Jun 04 2014 - 09:30:02 PDT
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