VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 22 2005 - 10:33:21 CDT

Kos,
  VMD doesn't have any limits on the number of trajectory frames you
can load other than that you have enough RAM to store them all. It's
clear from what you've said so far that you're unaware of the RAM
requirements to load large trajectories in VMD. I've loaded 32GB
trajectories on machines that have enough memory, so believe me,
it can be done. But, if you don't have the memory, you will have
to either load only a subset of frames, or you'll have to process them
with your scripts one-frame-at-a-time. I have several suggestions below
which I hope will clarify things to you and others:

1) If the DCD file size on disk is larger than your computer's RAM,
   you won't be able to load all of it into VMD at once.
   i.e. if you have 512MB of RAM, but a 2GB DCD file, there's no way VMD
   will load it in its entirety. You will have to load a subset of frames
   or process them one-at-a-time (see below).

2) If you know you don't have enough memory to load the entire file,
   you will have to load a subset of frames.
   If you're loading the DCD file for visualization, use the "stride"
   parameter in the "Frames" area of the molecule file browser window
   (file loading window) to skip an appropriate number of
   frames to bring it within the amount of RAM your machine has.
   This way you can visualize the entire trajectory, but you will be
   skipping frames as you watch. If you have 512MB of ram, but want
   to view a 2GB DCD file, you need to set the "stride" value to at
   least 4, best 5 to be safe.

3) If you're using VMD purely for analysis, you can run it in text mode
   with 'vmd -dispdev text'. Also, for simple analyses that don't require
   _all_ of the trajectory frames to be loaded at once, you should be using
   the "BigDCD" script in the VMD script library, which is an
   easy-to-use method for doing analysis on trajectories that are FAR
   too large to fit into physical memory. The script is located here:
     http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/

4) If you want VMD to load the DCD file as fast as possible, select
   the "load all at once" option in the "Frames" area. This will cause
   VMD to spend 100% of its CPU cycles loading the trajectory file before
   continuing, rather than the default behavior which is to load the
   trajectory file in the background so you can begin viewing it immediately.

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 21, 2005 at 09:29:21PM -0400, Kos wrote:
> Hi,
>
> We analyze large trajectory files with SALT IONS, WATERS, APROTININ (30000 atoms) produced by NAMD. We run them in a linux cluster and we analyze them in dual Intel Xeon system with VMD (Windows XP) using Exceed- (X-Windows). As long as the .dcd files are small around 300MB we didn't encounter problems analyzing them with X-VMD(Exceed) or even ftp the .dcd files in the Windows PC from Linux OS and analyze them directly with VMD for Windows.
>
> The problem is that when we analyze large 1ns .dcd file the X-VMD dissapears/crashes and can't read. When we transfer the files to Windows PC and try VMD there error for the trajectory file:'can't load , can't read the time etc'. Are there limitations in VMD? I noticed that for 10000frames is very slow to load and crashes.
>
> Is CHARMM an alternative solution to these problems and can treat large files faster because doesn't need graphics? A general question: Is CHARMM a more advanced package for MD analysis although not so friendly and how does compare in the postprocessing part with VMD?
>
> kos
>
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-- 
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