VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 21 2004 - 10:31:29 CDT

Lance,
  How are you setting those variables you mention? It should be
easy to free up their memory if you write your scripts properly.
Do you have a particular script you are running besides the
trajectory smoothing script?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 20, 2004 at 02:20:24PM -0500, Lance Pickens wrote:
> I am using the pre-compiled version of VMD 1.8.2 on an Apple using OS
> X v10.3.4 on a
> dual G5 system with 512mb of ram. My trajectory is 30mb in size.
> Tkcon becomes very sluggish, and so does VMD once the trajectory
> average has been completed, it can take several seconds for the Tkcon
> window to respond to commands. When I said 'reset' Tkcon I was hoping
> on clearing the memory since I have set several variables which
> contain large chunks of my trajectory.
>
> Lance Pickens
>
> On Tue, 20 Jul 2004 11:01:54 -0500, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Lance,
> > What version of VMD are you running, and on which platform?
> > How much memory does your computer have? You should have at least
> > as much _free_ memory as the size of the trajectory file you're
> > going to analyze if you want VMD to perform very well. If you're
> > using an old version of VMD you may have encountered a memory leak,
> > but hopefully not, more likely it is an issue of how much free memory
> > you've got. You asked about how to 'reset' TkCon, can you be more
> > specific about what you want to do to it?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Jul 19, 2004 at 08:29:31PM -0500, Lance Pickens wrote:
> > > I have been using the script (Trajectory_Smooth) from the script
> > > library to calculate my average structure from a trajectory. The
> > > problem is after the calculation is done VMD becomes very very
> > > sluggish. There are only 500 frames in my trajectory so it is not
> > > exremely large. Is there a way to reset tkcon?
> > >
> > > thanks,
> > > Lance Pickens
> > >
> > > Illinois Institute of Technology
> > > Chicago, Illinois
> >
> > --
> > 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
> > 

-- 
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