[gmx-users] (no subject)

Group Gro groupgro at yahoo.com
Sun May 5 11:10:40 CEST 2013

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?

Thanks alot.

S. Faraji

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