From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Dec 10 2014 - 08:44:22 CST
Do the two groups overlap significantly, or can you envision defining a
tilt variable between the group that comprises both and the axis itself.
Giacomo
On Dec 10, 2014 9:41 AM, "Jeff Comer" <jeffcomer_at_gmail.com> wrote:
> Oops, I understood that the change was made the previous day. But
> thanks! centerReference now works as I would expect.
>
> By the way, the reason why I am using centerReference on an angle is
> that is it is part of a solution originally suggested by Jérôme to
> implement the angle between two atomic groups and a fixed axis. For
> example, this is the angle that a vector from group2 to group1 makes
> with the z-axis:
>
> angle {
> oneSiteSystemForce
> group1 {
> atomNumbersRange 1-21
> centerReference on
> refPositionsGroup { atomNumbersRange 44-68 }
> refPositions (0,0,0)
> }
> group2 {
> atomNumbersRange 44-68
> centerReference on
> refPositions (0,0,0)
> }
> group3 {
> dummyAtom (0,0,1)
> }
> }
>
>
> –––––––––––––––––––––––––––––––––––———————
> 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 Wed, Dec 10, 2014 at 7:31 AM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >
> > The 2014-12-10 nightly build with this issue fixed is posted now.
> >
> > Jim
> >
> >
> > On Tue, 9 Dec 2014, Giacomo Fiorin wrote:
> >
> >> 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 — 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
> >>>
> >>> –––––––––––––––––––––––––––––––––––———————
> >>> 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
> >>>>>
> >>>>>
> >>>>> –––––––––––––––––––––––––––––––––––———————
> >>>>> 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/
>
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