RE: SMwST RATTLE Algorithm

From: Vermaas, Joshua (
Date: Wed Sep 25 2019 - 09:42:53 CDT

How far did it get into the 6th run before crashing? Oftentimes you can just restart from the restart files and everything will continue on as normal. If this works, I chalk it up to a temporary hardware goof or a particularly unlucky draw from the random number generator and go on with my life. :) If, however, it is consistent, then some more introspection is required to see what specific feature is causing this problem.


On 2019-09-24 15:35:16-06:00 wrote:

Dear NAMD users,
I have been using the SMwST method, following the "Exploring Complex Conformational Transition Pathways" tutorial, to refine the pathway of the separating of two domains of a protein from a "closed" to an "open" state. I have so far successfully ran 5 jobs, overall about 350 iterations, with this system. However, in my 6th job, the 152nd (of 250) replica changes conformation in a very drastic and unexpected way, it seems that a torque is applied to the protein somehow. This results in clashes with the structure, and I get an error (Constraint failure in RATTLE algorithm for atom 4862). This distortion only happened in the one replica as far as I can tell, and it happens around the end of the 6th job rather quickly. I have checked the restart files from the 4th job and don't see anything obviously wrong.
I would appreciate any suggestions, at this point I may try running this job again but I think I may run into a similar problem. Please let me know if you would like any more information. Thank you so much for your time.
Best regards,

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