[Chimera-users] file size of a trajectory

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 10 11:27:15 PDT 2015


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
>> _______________________________________________
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>> Chimera-users at cgl.ucsf.edu
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> 
> 
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