[gmx-users] REMD: after replica exchange breakdown
Mark.Abraham at anu.edu.au
Wed May 11 05:20:33 CEST 2011
On 05/11/2011 02:32 AM, SebastianWaltz wrote:
> Dear GROMACS User,
> I'm running a REMD MD of 32 replicas. It worked for the first few
> replica exchanges. After 30ps again two replicas were exchanged and I
> received the Error:
> x particles communicated to PME node y are more than a cell length out
> of the domain decomposition cell of their charge group
The only rationale I can see is that a velocity was scaled after
exchange that was now large enough to lead to the normal sort of
exploding system. Was the exploding replica going up in temperature? How
did you equilibrate the systems?
> I am using NVT assembles for each replica with a exchanging interval of
> 5ps. For each replica I use 4 processors. Constraint are only the bonds
> to hydrogens (constraints = hbonds). Using PME for electro static.
Information like GROMACS version, simulation system dimensions and
contents would be useful. What replica temperature distribution exists?
> When running each replica for its own everything is working fine,
> nothing is blowing up like one would expect after getting the above Error.
Good trouble-shooting :) You'd have been told to try this otherwise...
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