[gmx-users] rdf at contact

[Faezeh Pousaneh]

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>
wrote:

> 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
>
>