Dear Sir,Thank you for your kind response.I am using this command to calculate RDF:
radial rdf-1 0.1 35.0 :17-29 :1 center1 center2
where should I use vector command ??
I am using Amber12 ptraj
Thank you
Saikat pal
On Wednesday, 7 June 2017 7:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 07 2017 - 09:30:03 PDT
