VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 07 2013 - 14:50:18 CST

Hi,
  The previous MacOS and Windows versions of VMD have been 32-bit binaries,
which means that only 2GB can be loaded, regardless of how much physical
memory the machine has. You could either use the 64-bit Linux version of
VMD, or you could skip every Nth trajectory frame when loading the trajectory,
or load a segment of the trajectory at a time. Any of those methods are
a potential solution currently. We plan to make 64-bit versions available
for MacOS and Windows in the near future.

Cheers,
  John Stone

On Thu, Nov 07, 2013 at 04:31:15PM +0100, Alexandre PERRET wrote:
> Hello everyone,
> I try to load a trr file containing 2000 frames (35 000 atoms) with the
> latest version of VMD on a Mac OS X computer but VMD stops at 1312 frames.
> The software does not crash and I have no error message. I used gmxcheck
> and several gromacs scripts and I could not find any problem with the trr
> file. I also tried to load the file with a Windows computer but the
> problem remains.
> This is a 3 Go file but I use a computer with 16 Gb of RAM, so I don't
> think it is a memory problem either.
> Do you have any suggestions ?
> Thanks in advance,
> Alex
> --
> Alexandre Perret
> PhD Student
> Groupe de Spectrometrie Moleculaire et Atmospherique - UMR CNRS 7331
> Universite Reims Champagne-Ardenne
> Campus Moulin de la Housse - BP 1039
> 51687 REIMS FRANCE
> alexandre.perret_at_etudiant.univ-reims.fr
> Tel : (+33/0) 3 26 91 33 66
> Fax: (+33/0) 3 26 91 31 47 

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