On Wed, Jun 7, 2017 at 12:29 PM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> 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
Remove the 'center1' keyword; that is calculating an RDF from the
center of of mass of all your ions which is almost certainly not what
you want. You should also add the 'volume' keyword; otherwise you will
be normalizing to bulk water density which is also probably not what
you want.
-Dan
>
> where should I use vector command ??
You don't need 'vector' unless you want the actual center of mass coordinates.
> I am using Amber12 ptraj
The 'center2' keyword is for cpptraj-only. I recommend upgrading to
AmberTools 17 and using cpptraj.
-Dan
> 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
>
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--
-------------------------
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 - 10:00:02 PDT
