[gmx-users] Re: RDF calculation

[Justin Lemkul]

On 3/7/13 3:54 AM, Keerthana S.P Periasamy wrote:
> Dear all I have two discrete residues which are being connected together by
> sulfur atom in each residue. I need to find how the density varies around the
> residues or atoms attached with the sulfur atom and the water molecules
> surrounding it.  for that I created a group by selecting the two sulfur atoms
> using the index file. By giving RDF command Can I select the group which I
> created by index file as first group and the system as second group. And also
> is it possible to have RDF for vacuum phase simulation. Thanks in Advance

You can select any groups you want for RDF calculations, around any central 
reference group you like.  You can probably do in vacuo RDF, though you probably 
have to use -nopbc.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================