Seeking Assistance for Creating Full Trajectory Movies from Tutorials 7.2 and 7.3

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Ehsan Mirafzali

Dec 2, 2023, 11:37:33 PM12/2/23
to westpa-users

I am currently working on tutorials 7.2 and 7.3 in WESTPA and am interested in generating full trajectory movies. However, I am uncertain about the process, specifically regarding the creation of a DCD file for the entire trajectory.

I have come across some codes that might be useful for this purpose, but they seem to require .h5 files for each iteration in traj_segs. Unfortunately, I do not possess these files and am unclear on how to generate them.

Could anyone provide guidance or advice on how to proceed with this? Any suggestions or instructions on creating .h5 files or alternative methods for generating full trajectory movies would be greatly appreciated.

Thank you in advance for your help!

Anthony Bogetti

Dec 3, 2023, 7:15:30 AM12/3/23

Create full trajectory movies in WESTPA 2.0 can be accomplished with the westpa.analysis module in Python. Please see this GitHub page for instructions: The commands above will be run from your WESTPA simulation directory and will retrieve the trajectory files (dcd, nc, or other format that is readable by mdtraj) present in your traj_segs folder.

One of the newer features in WESTPA 2.0 is the storage of trajectory coordinates in h5 files instead of the native dcd, nc etc. The resulting h5 files take up significantly less disk space, and there are methods for retrieving the h5 coordinates in the link I have pasted above. The h5 file coordinate storage feature is not ‘on’ by default, please see this WESTPA wiki page for how to enable it for your simulations:

Please feel free to write back with any further questions.


On Dec 2, 2023, at 11:37 PM, Ehsan Mirafzali <> wrote:

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