VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 22 2005 - 10:21:17 CDT

Marc,
  VMD _DOES_ implement 4) already!!! (quite some time ago)
You need to set the fields in the "Frames" area of the molecule
file browser window. By setting "first", "last", and "stride"
you can load only a subset of the frames in your DCD file.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 22, 2005 at 10:15:17AM -0400, Marc Q. Ma wrote:
> Kos,
>
> Some sugestions:
>
> 1. Use a computer system with larger memory. 1, 2, 4GB. The larger, the
> faster.
>
> 2. When you produce the trajectories, save less frequently, say every
> 1ps per frame. Do not do it every 10fs per frame.
>
> 3. Or you may save as often as you wish (for whatever purposes), but
> you need a DCD_SPLITTER program to split the DCD files -- say save
> 1/10 of total number of frames to new files, and load these new files
> for analysis.
>
> 4. This maybe a nice feature, however, VMD still does not have: when a
> user load a dcd file, let the user control how many frames to load, how
> many frames to skip -- similar to what is provided for "Delete Frames"
> after all frames are loaded. This way, researchers can quickly check
> the trajectories without loading all frames.
>
> All above is related to allowing VMD to have ample computer memory to
> show graphics.
>
> John: Do you think (4) is a good feature to be added to VMD? I think it
> will be cool. Currently, my group is using Suggestion #2. This is not
> the best solution since the more we save, the more we can infer from
> our simulations.
>
> Marc
> On Apr 21, 2005, at 9:29 PM, 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