[Chimera-users] file size of a trajectory

MPI mpi566 at gmail.com
Wed Jun 10 12:24:37 PDT 2015


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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