[AMBER] Radial Distribution Function of Waters with respect to a particular Atom

From: <diego.soler.uam.es>
Date: Wed, 14 Nov 2018 11:11:06 +0100

Hello All,

I am trying to extract a Radial Distribution Function (RDF) from a
simulation. My topology and parameter file is mol.prmtop, and my
coordinate file is mol.coord. The system is basically a DNA with a lot
of waters around. I want to compute the RDF of waters with respect to
a particular atom, atom number 179. I am using this script:

parm mol.prmtop
trajin mol.coord
radial RDF 0.1 100 :WAT .179

and running it with "cpptraj -i cpptraj.in". But the result looks
very weird, because the RDF goes to zero instead of going to one, so I
guess I am doing something wrong, but I cannot fix it.

Thanks in advance for your help!

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Received on Wed Nov 14 2018 - 02:30:02 PST
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