From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Dec 10 2014 - 08:41:06 CST
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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