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

[Justin Lemkul]

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:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

-- 
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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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