[gmx-users] Problem with center-of-mass RDF and subsequent coordination number calculation

[André Farias de Moura]

Why should it be considered either wrong or weird? It seems a regular COM
g(r) plot to me.
Andre

On Fri, Jun 2, 2017 at 11:17 AM, Apramita Chand <apramita.chand at gmail.com>
wrote:

> Dear All,
>
> I want to calculate the COM RDFs between my peptide and water for which I
> have used the -com option in gromacs.(Also tried with -com and -rdf
> res_com).
>
> It generates a wierd RDF which does not look correct. I want to take the
> first minimum and use the -cn option to get the coordination number.
>
> The images for the RDFs are attached herein
>
> (1.https://drive.google.com/open?id=0B3bLwssa-3P7QzdSeUJEZWVYbW8
>
> 2. https://drive.google.com/open?id=0B3bLwssa-3P7SC1LaEFqWjVCc1k).
>
> What could be possibly wrong? The atom-atom RDFs are coming out well but
> not the COM ones.
>
> Additionally,
>
> If I use the -cn option of gromacs, it shows the cumulative CN right? Which
> means if I see the number at 0.257(say that's the cut-off), the number
> corresponding to it would be the coordination number. Am I right?
>
> What if I integrate the rdf using g_analyse -integrate option ?
>
> Any ideas on how to do the integration in Gromacs?
>
>
> *yours sincerely*
>
> *Apramita*
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090