[gmx-users] rdf at contact

Faezeh Pousaneh fpoosaneh at gmail.com
Thu May 31 12:08:12 CEST 2018

I will be grateful if some one can reply my question,

Best regards

On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh <fpoosaneh at gmail.com>

> Hi,
> I have a system of similar molecules, I would like to obtain the rdf at
> contact (meaning, at surface of one particle).
> What I try is; I make an index file containing only central atoms of all
> molecules, then I run:
> gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0
>  -b   14000
> ref 0 is a single atom
> ref 1 is rest of atoms
> Then, I find the rdf value at r=contact (radius of a molecule) from
> rdf.xvg file.
> My problem is I get very different values  for different time intervals
> (after equilibrium) . Why is that so?
> I appreciate if sb can help.
> Best regards

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