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 using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the system stops and i got this fatal
error:
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 steps
setted in the mdp file, but again I got the same error.
What should I do to overcome this problem?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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