VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 08 2013 - 09:02:16 CST

Alex,
  Interesting. That makes it sounds like your trajectory file may
be corrupt in some way. Are you able to process the TRR file with any of
the Gromacs tools, or do they report errors as well?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 08, 2013 at 08:43:41AM +0100, Alexandre PERRET wrote:
> Hi,
> Thank you for your answer.
> I tried to skip every Nth trajectory frame and load a segment of the
> trajectory but VMD still stops at the same frame (1312). For instance, if
> I load a segment from the 1000th frame to the end, VMD loads only 312
> frames.
> Thanks,
> Alex
> Le 7 nov. 2013 `a 21:50, John Stone a ecrit :
>
> 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/
>
> --
> 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/