Re: FEP error "atoms moving too fast"

From: Chris Chipot (
Date: Sun Jun 04 2006 - 16:01:23 CDT


there are at least three possible diagnostics for the problem you are

a) your system has been improperly equilibrated;

b) the list of excluded atoms is incorrect, so that the topologies of
    the initial and the final states do see each other when they never
    should. I would also check the internals common to the two states;

c) the time step is too large;

and any combination of the above.

There is a clear misunderstanding on the choice of delta lambda here.
An improperly chosen increment of the coupling parameter is unlikely
to cause a simulation to crash, unless there is an obvious flaw in the
definition of your system. Too large a delta lambda will simply result
in an absence of low-energy configurations of the target state that
are also configurations of the reference state - hence an absence of
convergence of your free energy calculation, but certainly not a crash

Chris chipot wrote:

> Dear all,
> I was running FEP calculation for a system about 50000 atoms
> (inclusing protein, DNA, cofactor, ions, and water). However, the
> calculation didn't even go through the first lambda change step (I set
> the change for each step to be 0.01). The error message I got is
> something about "atoms moving too fast" and after some iterations the
> energy change goes to inffinity. Is it because the change of
> lambda for each step is still too large for my system or something is
> wrong with the setup of the calculation? How should I check it?
> Thanks a lot!
> Jeny


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


     Science without management is worse than management without science

                                                        N. G. van Kampen

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