Re: about normal mode analisys

From: Jojart Balazs (jojartb_at_pharm.u-szeged.hu)
Date: Fri Jun 29 2007 - 16:13:27 CDT

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Dear Sławek,

As i know in normal mode analysis you use one coordintae file. The
quasiharmonic analysis is performed on the trajectory file. For this
calculation you can use ptraj, which is available free of charge from:
http://www.chpc.utah.edu/~cheatham/ptraj.html, and for a dexription
short (very!!!!) introduction to quasiharmonic analysis:
http://dasher.wustl.edu/bio5476/labs/lab-05/x492.html
hope this helps.

Balazs

Sławek Orłowski írta:
> Hi all!
>
> Does anyone has any experience in normal mode analysis with NAMD? I
> wonder is there any chance to use *.dcd trajectory file to do that?
>
> TIA
> Slawek Orlowski
> Theoretical Molecular Biophysics Group
> Faculty of Physics Astronomy and Informatics
> Nicolaus Copernicus University
> Torun, Poland
> home page: http://www.fizyka.umk.pl/~bigman/
>
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