[gmx-users] Error in minimisation

Justin Lemkul jalemkul at vt.edu
Sat Feb 1 16:41:37 CET 2014

On 2/1/14, 2:21 AM, hasthi wrote:
> Dear GROMACS users,
>                                    I am running membrane protein simulation.
> I have shrunk the area with the help of inflate.pl script.When I run energy
> minimisation I get this following error...
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot=         -nan Fmax= 9.20610e+05, atom=
> 5449
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.1
> Source code file: /home/guest/gromacs-4.6.1/src/mdlib/pme.c, line: 827
> Fatal error:
> 2 particles communicated to PME node 6 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> What might be the cause for this? I could not figure it out. Please help me
> out!!

You have an extremely large force on atom 5449, as the output above states.  The 
structure is so unstable that it cannot be minimized.  You will have to 
investigate the source of the problem based on whatever you have done previously 
and by visual inspection of the problematic atom(s).



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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