[gmx-users] g_rdf with exclusions

[Justin Lemkul]

On 10/19/15 4:36 AM, Pallavi Banerjee wrote:
> Hello all,
>
> I have a coarse-grained system of a single-chain polymer in water. I need
> to get the non-bonded potential between beads of the polymer from the rdf.
> For this I need to specify to g_rdf to not include the interaction between
> beads that are connected by bonds and angles. I use the following to do so:
> g_rdf -f cg.trr -n index.ndx -s topol.tpr -rdf atom -o rdf_A_A.xvg
>
> Is this the right way?
>

Depends on what the value of nrexcl is in the topology.

-Justin

-- 
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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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