[gmx-users] system is not well equilibrated -Reg

[Justin Lemkul]

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

-- 
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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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