[Chimera-users] Viewing Gromacs 4.6.5 trajectories

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 26 13:49:44 PDT 2014


Hi William,
	Chimera shows the 4.6 trajectories I have on hand without problem, and there shouldn't be any incompatible changes between the 4.6 and 4.6.5 releases.  Therefore I think I'm going to need (some of) your data to figure out the problem.  Can you send me your .tpr file and a few frames of your .xtc/.trr file?  You can write out a .xtc/.trr of just the first few frames of your trajectory with Gromacs' trjconv tool with the -dropover flag.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Mar 25, 2014, at 12:20 PM, William McDonald wrote:

> Hello Chimera users,
> 
> I recently upgraded my gromacs simulation software from 4.5.5 to 4.6.5; however, when I attempt to load a new simulation trajectory (either a .xtc or .trr file), Chimera allocates ~13GB RAM causing my machine to swap, and Chimera never loads the trajectory. The old trajectories from gromacs 4.5.5 load with out any problems. Has anyone else experienced this?
> 
> I am using 64 bit Chimera 1.8.1 on a dual quad-core Mac Pro running OS 10.6.8. The simulation has ~50000 atoms of protein, lipid, and water and is 1ns long.
> 
> -- 
> William J. McDonald
> Postdoctoral Scholar
> Department of Chemistry and Biochemistry
> University of California, Santa Cruz
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