Hi Kelly, VMD is very much designed to handle trajectories well, whereas ChimeraX is more of a jack of all trades and lacks some of the MD-focused optimizations that VMD has. For instance, ChimeraX uses higher-precision floating point numbers than VMD, so that is a factor of 2 in memory use in VMD's favor right there. Also, VMD reads trajectory coordinates in the background, and therefore can begin to show a trajectory quickly whereas ChimeraX reads the whole trajectory before displaying it. So VMD will definitely be able to handle larger trajectories than ChimeraX. To figure out roughly whether ChimeraX will be able to handle your trajectory, multiply 24 (bytes) x #atoms x #frames and compare that to the size of your computer's memory. You could cut down on the total memory use by using the "step" argument of the open command to read only every Nth frame, but for some coordinate formats it will still temporarily read all frames, which could still be problematic if the trajectory is massive. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 6, 2024, at 3:47 PM, Mcguire, Kelly via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories?
Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego
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