Re: colvars angle centerReference

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Dec 10 2014 - 07:31:11 CST

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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