VMD-L Mailing List

From: Alexandre PERRET (alexandre.perret_at_etudiant.univ-reims.fr)
Date: Fri Nov 08 2013 - 01:43:41 CST

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 à 21:50, John Stone a écrit :

> 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 Spectrométrie Moléculaire et Atmosphérique - UMR CNRS 7331
Université Reims Champagne-Ardenne
Campus Moulin de la Housse - BP 1039
51687 REIMS FRANCE
alexandre.perret_at_etudiant.univ-reims.fr
Tél : (+33/0) 3 26 91 33 66
Fax: (+33/0) 3 26 91 31 47