On Thu, May 13, 2010 at 9:15 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear community,
> After my simulation is over I am extracting the
> snapshots from .mdcrd file in PDB format. I am using the coordinates from
> each snapshot for farther analysis. Now is it necessary to do a RMS fit
> before extracting the snapshots by trajout command. Thank you in advance
> for
> your useful suggestions.
>
That entirely depends on what you're trying to learn. Sometimes an RMS fit
is necessary other times it's not (and in fact, I'm sure there are some
instances in which you definitely don't want to do it). Keep in mind that
ptraj is very capable of doing a large amount of data analysis by itself, so
writing out PDBs to do this is not strictly necessary (unless, of course,
you're using in-house scripts of some sort that only processes PDBs).
Good luck!
Jason
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu May 13 2010 - 07:30:07 PDT
