To calculate the center of mass of selected atoms see 'vector' command
with the 'center' keyword.
To calculate the RDF of the center of mass of a residue to ions you
can use the 'rdf' command with the first mask selecting ions, the
second selecting your residue, and use the 'center2' command to
specify center of mass of the second selection. See the Amber manual
for full details on these commands.
-Dan
On Tue, Jun 6, 2017 at 10:56 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote:
> Dear Amber users,
> How can I calculate the center of mass of a molecule from trajectory file (mdcrd)?
>
> If I have a system consisting of DNA and Ion, I want to calculate Radial distribution plot of Particular One residue like the center of mass of guanine with the ion.Is it possible?.
> In Amber 2015 manual page no 546 there is a command for the center of mass. If I use this command can I get the center of mass trajectory file for a particular atom ??
> please help me out .
>
> Thank you
>
> Saikat Pal
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Tue Jun 06 2017 - 09:00:02 PDT
