[gmx-users] system is not well equilibrated -Reg
jalemkul at vt.edu
Tue Dec 4 20:26:04 CET 2012
On 12/4/12 1:20 PM, venkatesh s wrote:
> Respected Gromacs Peoples,
> i got following error in the step mdrun nvt
> 1 particles communicated to PME node 1 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.
> i searched gmx user regarding the error but i cant get solution
> i understand Blowing up concept (
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up) before nvt npt
> itself error arise what i want do ? rectifying the problem
> (i followed protein&ligand tutorial
> SYSTEM INFORMATIONS
> ff :GROMOS96 43a1 force field
> ligand -->prodrg ,antechamber (charge)
> FOUR PROTEIN (USING :CHAINSEP -TER ) ONE LIGAND
> TOTAL NUMBER OF ATOM & RESIDUE
> chain #res #atoms
> 1 'A' 661 5352
> 2 'B' 686 5550
> 3 'Z' 4 4
> 4 'C' 148 1236
> 5 'D' 225 1706
> 6 'E' 236 1817
> 7 ligand 45
With this level of complexity, you're searching for a needle in a haystack.
Separate each component and attempt to simulate it, starting with the ligand to
check the integrity of its topology.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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