Dear all,
yesterday I reported that, in RXSGLD runs, I was finding a serious discrepancy between the potential energy as computed by the REMD part of the engine and that computed by sander. I finally narrowed
down the origin of the problem, and I am reasonably certain that it has to do with RESPA. In fact, if I stop using it (nrespa=1), then the discrepancy completely disappears. For sake of completeness,
I note that the behaviour persists regardless of system size. For example, it even happens with pentapeptides. The discrepancy can be huge: in my system of interest, the "correct" potential energy is
-2157 kcal/mol, whereas the replica exchange engine computes it as 13257 kcal/mol (*positive*). Obviously, this also indicates that the exchanges happen or are rejected according to wrong energies,
and, therefore, the final trajectories are more or less nonsense.
I strongly suspect that this behaviour is due to the REMD engine computing the energies at step numbers that are not multiples of nrespa, thereby getting meaningless results.
So, is this a bug, or is RESPA not supposed to be used in REMD runs?
Cheers,
Charo
--
Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
UK
https://charodelgenio.weebly.com
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Received on Sat Jan 30 2021 - 03:30:02 PST
