Problem with FEP simulations

From: Luba Simhaev (
Date: Mon Feb 01 2021 - 02:48:14 CST

Dear NAMD users,
I'm trying to perform alchemical FEP simulation to a system consisting of a
membrane protein, which is an ion exchanger. Prior to FEP, the system was
equilibrated for 250 ns. Although while I'm turning to FEP calculations,
they are halted due to "Constraint failure in RATTLE algorithm" error.
I know that this error indicates an unstable system,but as I mentioned the
system was equilibrated, and by visual inspection seems to be stable.
Could you please suggest how to solve this problem?

I would appreciate your help.

Dr. Ischakov Simhaev Luba, Ph.D.
Computational assisted drug-design unit
*Blavatnik Center for Drug Discovery*
Cohen-Porter Family United Kingdom Building
(Britannia), 1st floor
Tel Aviv University, Ramat Aviv
Tel Aviv, Israel, 6997801
Tel:+972-3-640-9842, 9654

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