[gmx-users] gold-protein simulation stop by error in equilibrum step

Justin Lemkul jalemkul at vt.edu
Thu Dec 6 21:16:29 CET 2012

On 12/6/12 3:12 PM, fatemeh ramezani wrote:
> hello
> I want to simulate gold nanoparticles with proteins. I've made ​​a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibrium, I am faced with the following error.
> application called MPI_Abort(MPI_COMM_WORLD, -1) - procesee 17application called MPI_Abort (MPI_COMM_WORLD, -1) - process Source code file:pme.c, line:538
> Fatal error:
> 2 particles communicated to PME node 17 are more than 2/3 times the cut-off out of the domain decomposition cell of the This usually means that your system is not well equilibrated.
> I've read previous questions and it is said that the system is unstable, but how do I equilibrium the system?
> I'm having this trouble in  equilibrium step Before beginning of MD.
> I equilibrate my system in 5 steps. by 5 em.mdp file that I named them em1.mdp, em2.mdp,em3.mdp, md100.mdp(temperature=100 k),md200.mdp(temperature=200k) and after these steps I do main simulation in 300k. I attached all mdp file.
> in md100.mdp steps, mdrun stops in middle of running and appear above error.

Please note that the mailing list does not accept attachments.

The failure is either due to an incorrect topology, inadequate minimization, or 
unstable .mdp settings.  Please also consult:




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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