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

fatemeh ramezani fr_750 at yahoo.com
Thu Dec 6 21:12:43 CET 2012

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 help me to resolve my problem
thank you

Fatemeh Ramezani

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