[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Sun May 5 13:35:10 CEST 2013

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.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list