From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Dec 10 2014 - 09:22:10 CST
My molecule is quite flexible, so I'm hesitant to use collective
variables based on reference coordinates. With tilt, my results would
depend on the choice of the reference conformation, when there's no
obvious reference conformation to choose. Of course, the angle also
says something about the conformations I'm expecting, but it's at
least easier to explain in a paper. Any thoughts on this?
Is there any advantage to including "hardLowerBoundary 0" and
"hardUpperBoundary 180"?
–––––––––––––––––––––––––––––––––––———————
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 8:44 AM, Giacomo Fiorin
<giacomo.fiorin_at_gmail.com> wrote:
> 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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