[gmx-users] RDF com

[Justin Lemkul]

On 10/17/15 5:32 AM, Deva Priya wrote:
> Hello,
>
> I am trying to calculate the rdf using the center of mass of a sulfonate
> group, SO3 with other SO3 groups in the system. The SO3 group is part of a
> bigger molecule. Is it appropriate to use
>
> gmx rdf -rdf mol_com to carry out this operation or  should I use the
>

This is correct.

> gmx rdf -yescom
>

Boolean options are never prefixed with "yes" so you would have gotten an 
obvious fatal error here.

> In each case I would specify the group that contains SO3 atoms twice for
> the rdf calculation.
>

Yes.

-Justin

-- 
==================================================

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

==================================================