From: Andrew Miglino (miglino_at_udel.edu)
Date: Wed Apr 10 2013 - 12:51:05 CDT
I'm relatively new to NAMD, but I've gone through both the FEP
tutorial and the ABF tutorial in preparation for running my own FEP
calculations to derive octanol/water partition coefficients (i.e.
deltaG_hydration - deltaG_solvation). I've been able to compute simple
deltaG_hydration values for methane as in the ABF tutorial on a single
core on my host computer. However, when I then apply the same method
to an OpenMPI implementation of NAMD v2.9 I get signal 11 errors and a
rapidly expanding box volume. This occurs regardless of solvent/solute
pair. I've seen the error "corrupted double-linked list", which I see
has an explanation but no clear solution.
In runs that do perform FEP calculations before showing a signal 11,
the .fepout file shows dG to be +99999999. Again, there is some
explanation for this in the troubleshooting guide, but since I've
tried to use the tutorial files in this setup to no avail, I strongly
doubt the error to be similar to "atoms moving too fast".
Are there suggestions as to how I can proceed from here?
Thank you for your time
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