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
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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
MPI -
Repic Matej