SMwST RATTLE Algorithm

From: Xander Gonzalez (
Date: Tue Sep 24 2019 - 16:28:24 CDT

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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