AMBER Archive (2009)
Subject: Re: [AMBER] RE: suggestions
From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Mon Jul 06 2009 - 20:29:22 CDT
The cross-correlation matrices ptraj generates are DCC maps.
For the analysis -
Hunenberger, P. H., A. E. Mark, and W. F. van Gunsteren. 1995.
Fluctuation and cross-correlation analysis of protein motions observed
in nanosecond molecular dynamics simulations. J Mol Biol 252:492-503.
and most of the papers that cite this paper.
On Mon, 2009-07-06 at 18:01 -0700, Ross Walker wrote:
> Hi Raja,
> Please post such questions to the AMBER mailing list, where I am cc'ing
> this. See http://lists.ambermd.org/ for signup details.
> You can accomplish what you want do by providing ptraj with a set of ranges
> for the trajin command. E.g. if you were writing to the trajectory file once
> every 1 ps, then for 12 ns you would have 12000 frames in your trajectory.
> Thus in ptraj you would specify:
> trajin foo.mdcrd 2001 12000 1
> To read every frame between 2001 (2.001ns) and 12000 (12ns).
> All the best
> From: Raja Pandian [mailto:chemistryraj_at_gmail.com]
> Sent: Monday, July 06, 2009 11:01 AM
> To: ross_at_rosswalker.co.uk
> Subject: suggestions
> Respected Sir,
> I need some suggestions for you.
> #I have 12ns trajectory. Now I want to split that into two parts, up to 2ns
> will be an equilibration period and then the remaining 10ns as mine
> production time. For this, how I can write the ptraj (ptraj.in) file?
> Because I want to do analysis on this production (10ns) time. How to
> remove/neglect the initial 2ns from mine 12ns trajectory?
> Here I have attached mine dyn.in file.
> #I would like to do the Dynamic Cross Correlation Map (DCCM) analysis.
> Searching AMBER archive showed that similar questions have been posted
> before but no answer. If it is possible, please send me the brief
> explanation about DCCM analysis and how to do that one?
> Thanks in advance for your suggestions.
> AMBER mailing list
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