From: Jason O'Young (joyoung_at_uwo.ca)
Date: Thu Jul 05 2007 - 11:39:50 CDT
I have a simulation using GROMACS parameters.
I have managed to get the simulation to run, however there are many
First of all, bond constraints eventually fail. When I look at the
data, the problem peptide "jiggles" with increasing speed until one
of the atoms (always the same atom) pretty much cannot be constrained
(I am using RigidBonds).
My question is: How reliable is the code used to port GROMACS files
I have looked at the code and could not find any wild reasons as to
why the simulation would fail. The simulation can run for 50 ns in
One possible reason I found was that NAMD takes both improper and
proper dihedrals and lists them as proper dihedrals when the
parameters are extracted. I am not too sure if this would cause the
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