VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 13 2000 - 22:30:44 CDT

Hi Surjit,
  Can you upload your files so that we can try them out and debug
the problem here? Please FTP them to:
  ftp.ks.uiuc.edu (as anonymous)
  bin
  cd pub/group/johns/incoming

If you could do that, it would help us debug the problem and we'd
be able to test your file with future revs of VMD. We don't have any
real local Charmm users here lately, so its hard to get test files for
this stuff... (I had been looking for more Charmm trajectories a while
back but was unable to collect any)

Also, just a suggestion: For your VMD-L posts, could you set your
mailer to send both ASCII and HTML versions of your email? My mail
reader was totally unable to display your message, although I would
have been able to read it despite being HTML. Some of us still use
(and even prefer!) plain old text-based mail readers. Also, it goes
into the VMD-L archive better if its plain old text.

Thanks!
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 11, 2000 at 08:54:16PM +0200, Surjit Dixit wrote:
<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Hi,
<br>I have been trying to visualize some trajectories generated by CHARMM&nbsp;(academic)
with some
<br>constraints in the system using VMD1.6a1. I wish to report an odd behaviour
by VMD (vmd1.4 behaves
<br>the same way too). My system is a protein solvated in water and the
trajectory is from a run where the
<br>protein is frozen and the waters are being equilibrated. VMD for some
reason does not show any of the
<br>waters as moving at anytime throughout the trajectory. My dynamics
simulations and trajectory seems to
<br>be fine, I have confirmed this by reloading the trajectory within charmm
itself for analysis and have also
<br>visualized the trajectory with gOpenMol. VMD is able to show the moving
configurations in the trajectory
<br>when no constraints are involved in the simulation.
<br>I wonder if anybody has noticed anything like this?
<br>I like the new interface of VMD, its more pleasant, thanks.
<br>Best regards,
<br>Surjit
<pre>--&nbsp;
Surjit B. Dixit, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Email: surjit_at_lctn.u-nancy.fr&nbsp;
Laboratoire de Chimie Th&eacute;orique, U.M.R. C.N.R.S. #7565, B.P. 239&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Universit&eacute; Henry Poincar&eacute;-Nancy I, 54506 Vandoeuvre-l&egrave;s-Nancy, France
Phone: 33-3-83.91.20.00 Extn:3588&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Fax: 33-3-83.91.25.30</pre>
&nbsp;
<p>&nbsp;</html> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078