Re: ABF question

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue May 25 2010 - 20:07:51 CDT

Hi Patrick, as you suggested already "specific combinations of colvars
components", means that a single colvar is built from multiple components,
that are summed together. "oneSiteSystemForce" renders these components
orthogonal for the sake of computing the system forces, for ABF or other
purposes (there are multiple ways to do that, so it's possible to make them
orthogonal by construction). The need to be orthogonal is also present when
there are multiple 1-component colvars (e.g. multidimensional ABF).

Say that for some reasons you have phi and psi dihedrals, which have three
atoms in common. You could define "oneSiteSystemForce" on phi to make it
orthogonal to phi.

Giacomo

---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
 giacomo.fiorin_at_temple.edu
---- ----

On Tue, May 25, 2010 at 2:38 PM, Patrick Yee <pyee_at_nd.edu> wrote:

> Jerome,
>
> Could you elaborate on what you mean by "building specific
> combinations of colvars components"? Do you mean when using
> multidimensional colvars or when using colvars comprised of more than
> one atom? Listing a few examples would be helpful.
>
> Thanks,
>
> Pat
>
>
> On 5/25/10, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> > Hi Arturas,
> >
> > > ABF tutorials does not use 'oneSiteSystemForce', while manual tells
> that it should be used with ABF and I would be doing it. Maybe by 'abf'
> declarations it is set by default ... Could someone clarify ?
> >
> > This is a bit technical. That option is never needed in simple cases
> > (one variable made of one component). It is only needed when building
> > specific combinations of colvar components, or running
> > multidimensional ABF on specific sets of colvars, when these are
> > defined based on sets of atoms that overlap. In any other case, you
> > don't have to worry about it.
> >
> > > Are there more examples of ABF with NAMD 2.7x apart tutorial ?
> >
> > There have been a few discussions on this list involving examples, you
> > can search the archive for them. If you need help achieving something
> > specific, we can discuss it on the list, which will increase the
> > number of documented examples.
> >
> > Jerome
> >
> >
>
>
> --
>
> Pat Yee - ChEg 2011
> Vice President of Am. Inst. of Chemical Engineers at ND
> Director of Interview Preparation for ND Consulting Consortium
>
>
> --
>
> Pat Yee - ChEg 2011
> Vice President of Am. Inst. of Chemical Engineers at ND
> Director of Interview Preparation for ND Consulting Consortium
>
>

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