Re: ABF simulation with extendedLagrangian on keeps crashing

From: Jérôme Hénin (
Date: Thu May 05 2011 - 17:02:56 CDT

On 5 May 2011 22:50, Ajasja Ljubetič <> wrote:
> 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?

Either way should work.

> 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?

Sure! (assuming of course the water is unconstrained) You won't get
any nonbonded contribution because of 1,3 exclusions, so you should
see just the harmonic angle potential, plus the Jacobian term.
Another option is to calculate the angle between 3 water molecules, or
even better, 3 noninteracting atoms - i.e. an ideal gas, in a periodic
box. Then the PMF will be just the Jacobian term (-RT *
ln(sin(theta))) but more importantly, the histogram should be flat!
(actually there can be a slight deviation due to the PBC, so you can
also try without - then Langevin dynamics with a significant coupling
will prevent the atoms from flying away too fast).


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