Re: ABF simulation with extendedLagrangian on keeps crashing

From: Ajasja Ljubetič (
Date: Thu May 05 2011 - 15:50:34 CDT

Hi Jerome,

As promised, I have just implemented ABF-specific routines for the
> angle component. I've only had time for very basic testing though. It
> looks fine, but it would be best if you can try it on a trivial system
> first. The two source files attached should be sufficient to enable
> it.

Thank you very much! Would you recommend that I compile this with the latest
CVS or the 2.8b1 release?
The most trivial system I can think of is the H-O-H angle bending of a
single water molecule. The shape of the free energy well should be parabolic
(as approximated by the CHARMM force field) with some small additions of the
H-H non bonding interactions, which can be calculated analytically for this
simple case. Would this make a good test case?

Your crashes might come from the singularity that occurs if one of the
> actual atoms gets too close with the dummy atom.

The dummy atom is 100 A away, so the other atoms can't get too close
(in Cartesian space).
There are actually two singularities that I forgot to consider: at theta= 0
and theta=180, where the phi angle is undefined (i.e. where three atoms of
the dihedral component become collinear). I'll try to do a run with more
restricted theta values.
But I find it strange, since I was applying the bias only to the theta
colvar (and calculating a 2D histograms of theta and
phi), shouldn't NAMD complain about a division by zero, instead of blowing
up velocities?

Thank you & best regards,

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