Re: Generating a gromacs topology file for analyzing NAMD trajectories

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Dec 06 2007 - 11:51:03 CST

Hi all,

I am curious as to what you mean by "PCA".

Richard
 
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55419-2959
rwoodphd_at_yahoo.com

----- Original Message ----
From: patrick wintrode <pat_wde2_at_yahoo.com>
To: L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
Cc: namd-l_at_ks.uiuc.edu
Sent: Thursday, December 6, 2007 8:54:25 AM
Subject: Re: namd-l: Generating a gromacs topology file for analyzing NAMD trajectories

Thanks for the replies. I was able to do PCA using just a pdb file and the .trr trajectory.

Now for another question. I did PCA on just the alpha carbons. When I generate a trajectory (of the alpha carbons) along the different components, it is displayed in VMD as just a collection of points. I've tried displaying as "trace", "tube" and various other options. Anyone know how to get VMD to draw connections between the alpha carbons?
 Thanks again.

Patrick L. Wintrode
Dept. of Physiology & Biophysics
Case Western Reserve University
Cleveland, OH 44106

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