Re: ABF Simulation

From: Jérôme Hénin (
Date: Wed Oct 19 2005 - 04:11:17 CDT


I believe that part of the problem lies in the atom indexes you pass to ABF
when defining the reaction coordinate. Your files indicate that you are using
atom indexes given by VMD, which start at 0. However, NAMD uses the PDB
convention for atom indexes, which starts at 1, so the atoms you pass to ABF
are not the ones you intended. This is a very common pitfall that probably
deserves to be more publicized in the community of NAMD+VMD users.

I don't have a clear idea of why you get that Tcl floating-point error,
though. Since one of the atoms is a hydrogen, it might be more prone to
numerical instability than a heavy atom, but this is not really a
satisfactory explanation to me. And since you are not constraining protein
hydrogens, issues involving constraints can be ruled out.

If anyone else experiences similar crashes, please tell me about it!


On Thursday 06 October 2005 16:13, Lionel Perrin wrote:
> Chris,
> The two atoms defining the reaction coordination belong to two distinct
> molecules, X1 corresponds to the Cgamma of an aspartate and X2
> corresponds to the C atom of the amidine function of a ligand.
> Hence, these two centers are not "chemically" bonded.
> In this case, should I apply a force constant at the border of the
> reaction coordinate and/or and external restraint ?
> Lionel
> Le mer 05/10/2005 à 14:58, Chris Chipot a écrit :
> > Lionel,
> >
> > could you tell us what atoms are involved in your reaction
> > coordinate ? Are these atoms chemically bonded to constrained
> > degrees of freedom ?
> >
> >
> > Chris Chipot

Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 87

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