[gmx-users] rdf

[Mark Abraham]

On 14/06/2011 10:11 PM, Nilesh Dhumal wrote:
> Hello,
>
> I have a system with 128 emi (cations) and 128 Cl (anions).
>
> I want to study is there any bifurcated interaction between hydrogen of
> cation and CL atoms or CL atom interacting with 2 different hydrogen of
> cation.
>
> For this I considered all CL atoms are distinguishable.
>
> I am thinking to run rdf between each hydrogen and each cl atom (RDF 128
> times).

There are various tools to measure distances between index groups. Check 
out chapter 8.

Mark

> In my index file I made 3 groups for 3 different hydrogen and 128 groups
> for 128 cl atoms.
>
> I have to run 128 * 3 = 384 times rdf
>
> Is this the correct way? Is there any other easier way to do this?
>
> I am using Gromacs 4.0.7 version.
>
> Thanks
>
> Nilesh
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