From: Priyanka Mondal (pmondal_at_udel.edu)
Date: Mon Apr 15 2019 - 09:45:52 CDT
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.
Department of Physics and Astronomy,
University of Delaware,
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