[AMBER] Amber 18 generates error: an illegal memory access was encountered launching kernel kNLSkinTest

From: Lucas, Xavier <xavier.lucas.roche.com>
Date: Tue, 1 Sep 2020 14:52:51 +0200


I'm running a standard NPT MD simulation in Amber 18 using scripts and
protocols that have worked well in previous projects, but as soon as the
calculations start it crashes and the error "Error: an illegal memory
access was encountered launching kernel kNLSkinTest" is printed in the
slurm logfile.

I found from previous posts that a likely issue was that there were
overlapping atoms in my input coordinates, so I ran the same system in NAMD
as a means to equilibrate the system for a few ns before attempting again a
run in Amber (using the same FF parameterisation). NAMD worked well but
using as input coordinates the system after 83 ns of simulation throws the
same error. Do you have any suggestions what else could be wrong here?

Thank you very much,

Dr. Xavier Lucas
*Senior Scientist in computational drug design*
Roche Pharma Research and Early Development
Roche Innovation Center Basel
Bldg. 092/3.92B.01
F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4070 Basel
Phone +41 61 68 89437
mailto: xavier.lucas.roche.com
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Received on Tue Sep 01 2020 - 06:00:02 PDT
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