[AMBER] OHE residue and crashing

From: Piia Kokkonen <piia.kokkonen.uef.fi>
Date: Fri, 8 May 2020 13:49:50 +0000


I am trying to run RNA simulations with 5' phosphates (and without) using the OL3 force field and Amber18. I can generate files and run some minimization with both systems, but the system with OHE (the 5' phosphate) will crash when I get to production simulations. Is this because I want to use the hydrogen mass repartitioning from parmed to speed up the simulations or am I missing something else?

The simulations without the 5' phosphate run fine with the hydrogen masses repartitioned at 4fs timestep, and I am using the same non-constrained starting structures so that shouldn't be the problem either. There is nothing visually wrong in the equilibration simulations (for 2 ns with 2fs timestep), the error message from the production simulation reads "Error: an illegal memory access was encountered launching kernel kNLSkinTest" which usually indicates that there is something crashing/exploding in the simulation.

Piia Kokkonen

Piia Kokkonen, Ph.D. (Pharmacy)
University of Eastern Finland
School of Pharmacy
P.O. BOX 1627
70211 Kuopio
Phone: +358 50 548 8376
Email: piia.kokkonen.uef.fi
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Received on Fri May 08 2020 - 07:00:01 PDT
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