[gmx-users] (no subject)

[Justin Lemkul]

On 5/5/13 5:10 AM, Group Gro wrote:
> Dear GROMACS users,
> I am working on protein-ligand complexes and when I run "mdrun -deffnm nvt.tpr -v" I run into this error:
>
> Fatal error:
> 2 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.
>
> I found the best docked position of my ligand by Autodock run and copied the best position of my ligand in a pdb format. Then I ran PRODRG to provide gro and itp files. I have tried different drugs as ligand and all of them are OK. I searched the mailing list and found other users have had this error. I understood that my system would be unstable. What should I do to solve this problem?
>

Start with a better topology.  PRODRG topologies produce bad results.

http://pubs.acs.org/doi/abs/10.1021/ci100335w

-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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