From: Hrant Gharabekyan (ghg_at_xalt.am)
Date: Tue Feb 08 2005 - 05:06:46 CST
I am simulating NPT ansamble of lipid bilayer system, in first time
after few steps running simulation give errors like
"ERROR: Constraint failure in RATTLE algorithm for atom 31275!
ERROR: Constraint failure; simulation has become unstable."
how I think, it was conditioned by the system size which shrinks very
fast, system patch size didn't reassigned up to restart.
After few restarts simulation normally run for 500ps. And continue
normally, but when I take last frame from .dcd, convert to pdb, and
start simulation with same conf using extracted pdb. Namd give
8 "constrain failure in Rattle algorithm" errors, after incrementing
margin to 16, there is only 1 error. I tryed to increment margin more,
change pairlistdist, disable UseFlexibleCell no effect.
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