Re: [AMBER] Script?

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 22 Oct 2013 13:25:03 -0600

Hi,

You can calculate this in cpptraj by calculating your vector(s) of
interest with the 'vector' action, then calculating the
autocorrelation with the 'timecorr' analysis, e.g.:

vector v1 .25 @26
timecorr vec1 v1 order 2 out v1.p2.dat

You may also be interested in the IRED analysis method of Prompers &
Bruschweiler, which is available by adding the 'ired' keyword to
'vector' and using the 'ired' analysis command; see the manual for
more details.

Hope this helps,

-Dan


On Tue, Oct 22, 2013 at 11:30 AM, Beale, John <John.Beale.stlcop.edu> wrote:
>
> Hello,
>
> Does anyone have a script that will calculate the P2 order parameter over the time course of a molecular dynamics simulation?
>
> Thanks!
>
> John
>
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Oct 22 2013 - 12:30:02 PDT
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