Fwd: w_run --oneseg

[Eduardo Jardón]

Hello,

I'm using westpa to track a distance between two domains in a receptor protein. I noticed in segment 34 the distance goes to zero as reported in the west.h5 file. Simulation is still running segments, and zero is not included in the bin's interval.  What I want to do is to update the reaction coordinate and perform analysis. Is that possible?

Do I have to re-run the the full trajectory? how can I use  w_run --oneseg to run only those segments with the wrong calculation of the distance coord?

cheers,

Eduardo

[Anthony Bogetti]

Hello Eduardo,

The best way to re-run those segments is to “truncate” your h5 datafile to a previous iteration.  This will allow you to cleanly change the reaction coordinate definition (including bin spacings/bounds) and resubmit your simulation.

Please see our wiki page on w_truncate for instructions.

Let us know if you have any further questions!

Anthony

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