[Chimera-users] file size of a trajectory

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 10 16:24:58 PDT 2015


My guess is that increasing your physical memory would likely help if your current memory is somewhat small, say 4GB, but probably not help much if it is already big, say 32GB or so.

--Eric

On Jun 10, 2015, at 12:24 PM, MPI <mpi566 at gmail.com> wrote:

> Hi Eric and Matej,
> 
>   Thanks for the comment.
> 
> Essentially, keeping a file size of trajectory < 1GB is one of workarounds.
> 
> I am curious if increasing system memory say 32GB  would help because
> I saw 64bit Chimera consumes system memory until it crashes.
> 
> Thanks,
> 
> Dewey
> 
> On 6/10/15, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> All very true.  One of the design goals of Chimera 2 is to work well with
>> very large systems, but it still won't be available for awhile yet.
>> 
>> The one thing I would add is to make sure you are working with the 64-bit
>> version of Chimera.  The 32-bit version is limited to 2GB of memory use.
>> 
>> --Eric
>> 
>>                        Eric Pettersen
>>                        UCSF Computer Graphics Lab
>>                        http://www.cgl.ucsf.edu
>> 
>> On Jun 10, 2015, at 2:20 AM, Repic Matej <matej.repic at epfl.ch> wrote:
>> 
>>> From my experience, Chimera does not seem to be suited for large system
>>> analysis, be it a trajectory or just a static structure (pdb, gro) with
>>> 100k+ atoms. Try to set the default representation to "wire" in
>>> preferences and use trjconv to make the trajectory smaller by skipping
>>> every tenth frame or so. Maybe even omit a part of the system (solvent,
>>> lipid) if that is feasible. However, these workarounds do not really
>>> address the underlying issue, which is that MD analysis does not seem to
>>> be exactly Chimera's strong suit (yet?). Therefore, I would suggest you
>>> use VMD (Visual Molecular Dynamics), which is a better tool for
>>> visualizing large MD trajectories.
>>> 
>>> Best,
>>> Matej
>>> 
>>> 
>>> 
>>> ------------------------------------------------------
>>> Dr. Matej Repic
>>> Ecole Polytechnique Fédérale de Lausanne
>>> Laboratory of Computational Chemistry and Biochemistry
>>> SB - ISIC ­ LCBC
>>> BCH 4108
>>> CH - 1015 Lausanne
>>> 
>>> ------------------------------------------------------
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 6/10/15, 06:41, "MPI" <mpi566 at gmail.com> wrote:
>>> 
>>>> Dear Users,
>>>> 
>>>> I use the lastest version of Chimera to read  trajectory (.xtc)
>>>> files output from Gromacs ver 4.6.5.   When a .xtc file size larger
>>>> than 2GB in most cases and 1GB in some cases,  Chimera gets choked and
>>>> crashed.   When a .xtc file size < 1GB, Chimera works very well.
>>>> 
>>>> I wonder if this is a limitation for reading Gromacs trajectory files.
>>>> Is there a solution ?
>>>> 
>>>> Thank you.
>>>> Dewey
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>>> 
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>> 
>> 
>> 
>> 
> 




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