NAMD Run Instabilities

From: Marc Gordon (
Date: Thu Sep 06 2012 - 08:15:58 CDT

Hi all

I've recently started running my NAMD sims on a cluster on campus as
opposed to on my local machine so that I can do a whole lot more a whole
lot quicker.

I uploaded the exact same config file and the various force field and
structure files onto the cluster and began some test runs just to be sure
that the results being produced were comparable to the stuff I was getting
on my local machine.

Long story short the results I get from these runs are inconsistent.

As an example I can start 2 identical runs and 1 falls over with some or
other instability error halfway through (usually "atoms moving too fast" or
"low global exclusion count" errors but it varies) while the other runs to
completion. Is this normal NAMD behaviour? Any idea what could be causing
this? I have had the poor admin for the cluster installing multiple
versions of NAMD to test this (2.8, 2.9 nightly build, 2.9 stable
precompiled, 2.9 stable compiled on the cluster) and they all seem to
follow a similar pattern (although the nightly build develops instabilities
with every run so far).

To give you some background I am simulating a dissaccharide, no water or
anything just the dissacch. The only thing that could be said to be beyond
the "totally vanilla carb sim" label is that I am using the colvars module
for some metadynamics sampling on the dihedral bond between the residues.

Any insights would be appreciated as right now I am tearing my hair out
with this problem.

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