Re: NAMD Run Instabilities

From: Chris Harrison (
Date: Thu Sep 06 2012 - 08:57:41 CDT

Dear Marc,

Please post a copy of your namd config file. How many total atoms are
in the system and how many cores are you using?

I suspect your problem may have more to do with "physical
instabilities" in the system that become more apparent when either a)
you're able to run longer due to running in parallel on the cluster, or
b) the metadynamics parameters in your config need some tweeking, or c)
the additional randomness from parallelization is introducing just
enough difference from the serial run to reveal the underlying
instability (which may still be from meta-D or other parameters that
need tweeking.)

On another note: Why are you running in vacuum instead of solvent? Are
you utilizing a dielectric other than 1? Running a charged sugar (if it
is charged or highly polarizable) in vacuum lacks the dampening provided
by solvent molecules and could potentially yield high forces.


Marc Gordon <> writes:
> Date: Thu, 6 Sep 2012 15:15:58 +0200
> From: Marc Gordon <>
> To: namd-l <>
> Subject: namd-l: NAMD Run Instabilities
> 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.


Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078               Fax:   217-244-6078

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