Re: AMBER: snapshots of MD trajectory

From: Xin Hu <hux.mail.rockefeller.edu>
Date: Fri, 27 Aug 2004 12:36:06 -0400

Hi Guanglei,
Could you please instruct me more details on the cluster analysis using
ptraj? I checked the manual of Amber8 and only found "average" command in
ptraj could be useful. Do you mean the "analyze modes" for cluster
anallysis?

Thanks for your help.


Xin

---
----- Original Message ----- 
From: "Guanglei Cui" <cuigl.csb.sunysb.edu>
To: <amber.scripps.edu>
Sent: Friday, August 27, 2004 11:27 AM
Subject: Re: AMBER: snapshots of MD trajectory
> You can use ptraj to extract snapshot and do cluster analysis. It's part
> of amber suite.
>
> Guanglei
>
> Xin Hu wrote:
>
> > Hello,
> > I have a question about the analysis of MD trajectory from Amber 8. How
> > can I extract all the snapshots (such as save as PDB file) from the MD
> > trajectory, and generally, is there a way to cluster these ensembles  of
> > MD snapshot?
> >
> > Thank you very much for your help.
> >
> >
> > Xin
> >
> >
> > ---
> >
> >
> >
> >
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Received on Thu Sep 02 2004 - 01:15:11 PDT