From: ALEXANDRE PERRET (alexandre.perret_at_etudiant.univ-reims.fr)
Date: Fri Nov 08 2013 - 10:35:24 CST

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/
>