[gmx-users] bond length deviation
czapla at rutchem.rutgers.edu
Fri Oct 26 00:56:56 CEST 2001
Your advice with handling Glucose with GLCA was very helpful. We have a
problem with two simulations we are running. One is a PDB file taken from
the protein databank of the crystal structure of our protein with glucose.
The other is a simple 4 peptide chain of glycine in a box with a Chloride
ion. Both seem to get this fatal error about the Bond Length deviating by
more than half about 50-150ps into the simulation.
I was wondering how this is so with the harmonic potential and
using only the standard residues with ffgmx. Maybe we have done something
to create this problem; we used a procedure similar to the gmxdemo file.
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