Ligand atoms moving too fast with FEP

From: Francesco Pietra (
Date: Thu Feb 15 2018 - 02:00:39 CST


While I had no problems so far with protein-ligand FEP, with a new similar
ligand, parameterized for charmm36 at the same quality level as before for
the other ligands, FEP crashed.

The new system had been subjected to charmm36 npt MD for 1,000,000 steps at
ts=1.0fs on a single node CPU-GPU box, reaching constant rmsd vs frame.
With frwd FEP, carried out on a nextscale cluster on two Broadwell nodes
(72 cores) at ts=1.0fs, the simulation crashed nearly immediately (within
19s) with three atoms of the ligand moving two fast.

What about resubmitting classical MD on the cluster for > 1,000,000 steps?
Or what could be better?

thanks for advice

francesco pietra

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