[gmx-users] RDF

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Tue Jul 11 19:38:59 CEST 2017

When I try to make an index group for the protein residue and the ligand molecule, the whole system is included in the index file. 

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 11 July 2017 18:06
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RDF

On 7/11/17 11:41 AM, Pandya, Akash wrote:
> Hi,
> I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that?

By using make_ndx or a suitable command-line selection when running gmx rdf (see gmx help selections, but make_ndx is often much easier to use/comprehend for very simple cases like this).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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