[gmx-users] rdf at contact

Dallas Warren dallas.warren at monash.edu
Thu May 31 04:34:13 CEST 2018

How noisy is the rdf i.e. what is the bin width, how many atoms etc?
Have you graphed the entire function?  That would be my first
suggestion of the cause.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 31 May 2018 at 00:45, 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
> --
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