Error while equilibrating AGNR nanopore + DNA system

From: Priyanka Mondal (
Date: Mon Apr 15 2019 - 09:45:52 CDT

Hello all,
I am a beginner in NAMD and I am trying to simulate DNA through AGNR
nanopore similar to tutorial DNA through Si3N4 in NAMD site. I have two
First, the minimization ran without error but when I opened trajectory
file, I saw the AGNR structure was distorted. I am not sure how to fix
that. Quick google search suggested that I might have to define a force
constant somewhere in parameter file. I am not sure how to do that.
  Secondly, I ran equilibration NAMD simulation anyway and there I
encountered the error "Warning: Low global exclusion count!",
"ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 58 pe 40).
and the simulation stops. I tried the following :
1> change langevinPistonTemp gradually so that there is gradual increase of
force and thus limit velocity of atoms
2> Change timestep to much smaller values
But none of these seem to work. It will be nice if someone can help me.

Priyanka Mondal,
Department of Physics and Astronomy,
University of Delaware,

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