Swarms Errors

From: Xander Gonzalez (xandergonz1_at_gmail.com)
Date: Fri Aug 16 2019 - 13:10:45 CDT


I have been trying to refine a pathway with colvars using SMwST, following
the "Exploring Complex Conformational Transition Pathways" tutorial, but
using my own structure. Originally I created 20 images from my non
equilibrium trajectory, but swarms ran for only a few iterations before one
replica stopped, in the log file for this replica was recorded "ERROR:
Constraint failure in RATTLE algorithm for atom 12757!". Soon after this
replica failed the rest stopped running as well. I thought that this may
have been a result of the accompanying image being faulty so I resampled
the non equilibrium trajectory to get 50 images, but got the same error in
another replica for the same atom. Next, I tried minimizing the
accompanying image, but then another replica for another image had this
error, this time with atom 12760. I am currently minimizing all 50 images,
and I am trying another run with margin set to 5 (as supposed to the
default 0). Could there be anything that I'm missing with this? Please let
me know if I can provide any other information about what I'm trying to do.
Thank you so much for your time.


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