Re: PCA calculation

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Feb 11 2008 - 11:34:07 CST

I was hit very hard by Peter's stone :)

You could also use ptraj, although I haven't used it for very, very long time.

Here is the link:

http://www.chpc.utah.edu/~cheatham/software.html

Cheers,
Michel

On Feb 11, 2008 10:38 AM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> *Real* programmers use matdcd
> (http://www.ks.uiuc.edu/Development/MDTools/matdcd/) and do it in
> matlab. ;-)
> But gromacs is the fast and easy way way.
> Peter
>
>
> Xu, Jiancong wrote:
> > Don't think so. One thing you can do is to convert dcd trajectory to any other format that can be read by gromacs, and use gromacs to calculate PCA.
> >
> > Jiancong
> >
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu on behalf of ramya narasimhan
> > Sent: Mon 2/11/2008 2:49 AM
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: PCA calculation
> >
> > Hi all,
> > Is it possible to calculate PCA for MD trajectories using NAMD?
> > Thanks in advance.
> >
> > Ramya.L.
> >
> >
> > ---------------------------------
> > Chat on a cool, new interface. No download required. Click here.
> >
> >
>
>

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