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
--
========================================
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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