[gmx-users] REMD: after replica exchange breakdown
sebastian.waltz at physik.uni-freiburg.de
Wed May 11 14:59:22 CEST 2011
On 05/11/2011 05:20 AM, Mark Abraham wrote:
> 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 did a NPT equilibration for each replica which leads obviously to
different volumes and looks like to cause some problems. If I use the
same volume for each replica it works fine.
>> 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?
I am using version 4.0.7. My system consists of a small peptide soluted
in ~1500 rigid CHCl3 molecules. System equilibrated with NPT and NVT
production run seems to work only if I increase the number of replicas
(32->64) meaning that I also decrease the difference of the volumes. The
temperature is exponentially distributed from 200 to 450K.
>> When running each replica for its own everything is working fine,
>> nothing is blowing up like one would expect after getting the above
> Good trouble-shooting :) You'd have been told to try this otherwise...
Thanks a lot
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