[gmx-users] g_rdf

[leila salimi]

Dear Justin,

Thanks. I have another question about coordination number ( the cumulative
number ). I am looking for RDF between two type of atoms, first is Ca ions
and the second group is Oxygen of side chains of peptide at solid/liquid
interfaces. I don't understand the integration of RDF. I expect the number
at first minimum of RDF might be around 2-3 but I got a very small around
0.1!
Then I tried with -surf mol option, because all Oxygens consist of one
molecule then the value increased to 1.6 !  I don't know the physics behind
this normalization and integration. Could you explain for me?
When we have two groups of atoms, the cumulative number is the average
number of coordination between two groups of atoms?

Regards,
Leila

On Mon, Feb 23, 2015 at 1:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/23/15 6:50 AM, leila salimi wrote:
>
>> Dear all,
>>
>> I have a question regarding radial distribution function. Does g_rdf
>> program work for non-cubic cell eg. triclinic?
>>
>>
> 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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