[gmx-users] RDF com

[Deva Priya]

Thanks a lot, Justin.

On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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