[Chimera-users] file size of a trajectory

Repic Matej matej.repic at epfl.ch
Wed Jun 10 02:20:30 PDT 2015


>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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