<WESTPA 2.0: Error while reading trajectories>

[Praveen Ranganath Prabhakar]

Dear WESTPA community,

Hope you are doing well. I am attempting to extract the trajectory of the 2nd walker from a particular iteration (10th iteration) from a WESTPA 2.0 simulation. The engine I am using is AMBER and I am storing my trajectories as .nc files. I am following the same protocol provided in the WESTPA 2.0 document.  Please find below the code snippet I had used.

run = Run.open('west.h5')

last_iter = run.iteration(10)

walker = last_iter.walker(2)

trajectory = BasicMDTrajectory(top=top) #top variable has the path to the topology file (.prmtop file)

traj = trajectory(walker)

When I run it, I am getting the below error and I am unable to resolve it. Request your help please :)

utf-8' codec can't decode byte 0xc8 in position 447: invalid continuation byte

Thank you.

Best,

Praveen

[Anthony Bogetti]

Hi Praveen,

You seem to be on the right track with your code snippet.  Can you try using the full path to your topology file (as a string) in the BasicMDTrajectory line?  Have you previously defined ’top’?  Also, you can try to manually set the file extension as ’.nc’ to see if that helps:

trajectory = BasicMDTrajectory(traj_ext=‘.nc', top=‘./common_files/your_top_file.top')

Please let me know if you run into any further errors with this.

Anthony

<image.png>

Thank you.

Best,

Praveen

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