VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 22 2013 - 23:42:45 CST

Hi,
  Can you try using one of the test versions of VMD 1.9.2 and
see if you have the same problem or not?:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 08, 2013 at 05:35:24PM +0100, ALEXANDRE PERRET wrote:
> Hello John,
>
> Yes, I am able to process the TRR file with the Gromacs tools and I
> used gmxcheck with the file and didn't get any error message.
> In the case of loading a fragment or skipping the Nth frames, VMD
> still has to read the entire trajectory file and then load the
> requested frames, isn't it ?
>
> Alex
>
> Message de "John Stone" <johns_at_ks.uiuc.edu>:
>
> >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/
> >
>
> 

-- 
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/