Re: Problem with FEP simulations

From: David Hardy (
Date: Tue Feb 02 2021 - 18:43:57 CST

Dear Luba,

As you point out, this does indicate some kind of instability. It is possible that you introduced the problem with your FEP parameter settings.

It would help if you provide more details on how you are running NAMD and how the error manifests. Even better if you could provide the files that are producing this error.

Best regards,

David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801,
> On Feb 1, 2021, at 2:48 AM, Luba Simhaev <> wrote:
> 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.
> Thanks,
> Luba
> -- 
> Dr. Ischakov Simhaev Luba, Ph.D.
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