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

[Apramita Chand]

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*