[gmx-users] A charge group moved too far between two domain decomposition steps
Dr. Vitaly Chaban
vvchaban at gmail.com
Tue Jun 11 15:27:00 CEST 2013
This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larger *spatially) system you simulate, the more likely it to appear.
The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.
Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 12:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/11/13 1:30 AM, Souilem Safa wrote:
>> Dear Gromacs users,
>> I tried to do the simulation of a single molecule in cyclohexane, I'm
>> gromos 53a6 force field for both molecules.
>> i did all the minimization steps. After npt, I runned for 25 000 000
>> just after around 100 000 steps, the system stops and i got this fatal
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>> Then I back again to npt step to equilibrate for longer time as the error
>> message said to me, I equilibrate for 500 000 steps instead of 250000
>> setted in the mdp file, but again I got the same error.
>> What should I do to overcome this problem?
> There are plenty of possible problems within your topology or .mdp
> settings. Unfortunately, you provided neither, but everything there is to
> say is fairly well summarized in the link.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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