[gmx-users] Automatic calculation of several RDFs

Dallas Warren dallas.warren at monash.edu
Fri Feb 15 00:10:08 CET 2019

Yes it is, write the script in what ever programming language you use. I
have one in python that takes a list of residues and atom names, then
generates all the RDFs between those. You can invoke gmx rdf in series, or
in parallel (which I was able to do using python).

Since your interested in time series, simply count through each command
increasing - b and - e by 1000.

Even more simply fill a text file with the list of rdf commands, one on
each line, make file executable, then execute it and let it run. No
programming language / skill required.

On Thu, 14 Feb. 2019, 4:18 pm Behnam Ghalami, <ghalamichoobar at gmail.com>

> Dear all
> I want to obtain  the change of RDFs for 1ns interval during simulation. My
> simulation time is 200 ns. Since my simulation box is large, it's time
> consuming. Is it possible to define a script to calculate RDFs one after
> another? Let me rephrase my question. Can I select the groups, which RDF is
> needed, in gmx rdf command?
> Thanks in advance,
> Best regards
> --
> Behnam Ghalami Choobar
> PhD Candidate in Chemical Engineering
> Amirkabir University of Technology, Tehran-Iran
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