Re: ABF Simulation

From: Lionel Perrin (lionel.perrin_at_cea.fr)
Date: Fri Oct 21 2005 - 04:03:02 CDT

Jerome,

Thank you for the answer, I knew about the index issue between NAMD and
VMD but I did not pay attention that time ! :-S
I have restarted the simulation with the "good" indexes and will tell
you the outcome of the ABF simulation.

thank's a lot,

Lionel

Le mer 19/10/2005 à 11:11, Jérôme Hénin a écrit :
> Lionel,
>
> 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!
>
> Jerome
>
> 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

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