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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/)
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
--
========================================
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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