From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Dec 09 2014 - 21:41:26 CST
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/
>
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