Hi,
On Wed, Jun 7, 2017 at 6:51 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> I want to know if I have a molecule like guanine which consist of H22,H21,N2,C2,N3,O6,H1,N1,C5,C6,C4,N7,H8,C8,N9 atom ,if I use this command for RDF calculation :
> trajin modified-125.mdcrd
> radial rdf-1 0.1 35.0 :1.H22,H21,N2,C2,N3,O6,H1,N1,C5,C6,C4,N7,H8,C8,N9 :17-29.K+
> Is it calculate the RDF plot center of mass of the Whole residue with ion ??
As I stated previously, to get the center of mass of atoms selected by
a mask in the 'rdf' command you need to use either the 'center1' or
'center2' keywords. Otherwise the RDF is for every atom in the mask. I
think this is explained reasonably well in the manual.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Jun 07 2017 - 07:00:03 PDT
