On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote:

I am simulating a peptide in TFE-water system. I am getting following error:
1 particles communicated to PME node 4 are more than 2/3 times the
cut-off out o f the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.

below is my em.mdp file

integrator      = steep
emtol           = 1000.0
emstep      = 0.01
nsteps          = 50000
nstlist         = 1
ns_type         = grid
rlist           = 1.2
coulombtype     = PME
rcoloumb        = 1.2
rvdw            = 1.2
pbc             = xyz

Please help me. Why this error has ocurred and what parameter should I
change to resolve it.

Likely the cutoffs are simply wrong, but you haven't said what the force field is. The other possible sources of problems during EM are (1) bad topology or (2) unreasonable starting configuration.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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