Re: colvars angle centerReference

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 09 2014 - 21:54:55 CST

The nightly builds are built late at night, and it is too early now.

The issue is that for angle and dihedral the coordinates are re-read prior
to calculating the variable, but the roto-translational fit doesn't get
updated. It hasn't shown up until your test because normally there is no
need to define a roto-translational fit for angle and dihedral, which are
invariant under roto-translations anyway.

Giacomo

On Tue, Dec 9, 2014 at 10:41 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:

> Jim, Giacomo, thanks. Using the nightly NAMD build, Colvars still
> seems to be ignoring "centerReference" for an angle. I'm assuming from
> Giacomo's response that my expectations were correct โ€” that applying
> "centerReference on" on each group of an angle colvar should yield a
> constant angle value, regardless of where the atoms go. It seems to be
> a problem within Colvars, so perhaps I should have posted this on the
> Colvars page (and tried the most up-to-date version of Colvars). But
> anyway, I've spent a little time trying to trace how centerReference
> is implemented in the Colvars code, colvarsatoms::b_center,
> calc_apply_roto_translation()... but so far I see no reason why the
> centering doesn't happen for an angle colvar.
>
> Jeff
>
> โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€”โ€”โ€”โ€”โ€”โ€”โ€”
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Tue, Dec 9, 2014 at 6:35 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
> > Hi Jeff, sorry for the late reply. Jim took a look at it, and you can
> > probably see the issue fixed in the latest CVS.
> >
> > Giacomo
> >
> > On Fri, Dec 5, 2014 at 4:00 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> I'm having some trouble using an "angle" colvar with "centerReference
> >> on". I think this used to work.
> >>
> >> As a test, I define a "distance" colvar by:
> >>
> >> colvar {
> >> name distFixed
> >>
> >> distance {
> >> group1 {
> >> atomNumbers 1
> >> centerReference on
> >> refPositions (3,0,0)
> >> }
> >> group2 {
> >> atomNumbers 68
> >> centerReference on
> >> refPositions (0,0,0)
> >> }
> >> }
> >> }
> >> I expect that this distance is always 3.0, and indeed it is.
> >>
> >> However, for "angle" colvar, it doesn't seem to work like this. I
> >> would expect the following to always give 90, but it does not.
> >> colvar {
> >> name phi6
> >>
> >> angle {
> >> group1 {
> >> atomNumbers 1
> >> centerReference on
> >> refPositions (1,0,0)
> >> }
> >> group2 {
> >> atomNumbers 34
> >> centerReference on
> >> refPositions (0,0,0)
> >> }
> >> group3 {
> >> atomNumbers 68
> >> centerReference on
> >> refPositions (0,0,1)
> >> }
> >> }
> >> }
> >>
> >> Is this a bug, or is there something that I'm missing?
> >>
> >> Thanks,
> >> Jeff
> >>
> >>
> >> โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€“โ€”โ€”โ€”โ€”โ€”โ€”โ€”
> >> Jeffrey Comer, PhD
> >> Assistant Professor
> >> Institute of Computational Comparative Medicine
> >> Nanotechnology Innovation Center of Kansas State
> >> Kansas State University
> >> Office: P-213 Mosier Hall
> >> Phone: 785-532-6311
> >>
> >
> >
> >
> > --
> > Giacomo Fiorin
> > Assistant Professor of Research
> > Institute for Computational Molecular Science (ICMS)
> > College of Science and Technology, Temple University
> > 1925 North 12th Street (035-07), Room 704D
> > Philadelphia, PA 19122-1801
> > Phone: +1-215-204-4213
> > https://icms.cst.temple.edu/members.html
> > http://giacomofiorin.github.io/
> >
>

-- 
Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213
https://icms.cst.temple.edu/members.html
http://giacomofiorin.github.io/

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:27 CST