From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 07 2015 - 14:00:02 CST
hardLowerBoundary and hardUpperBoundary only have an effect on expandable
and self-adjustable grids, currently implemented only for metadynamics.
Giacomo
On Wed, Dec 10, 2014 at 10:22 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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--047d7b3a94fe4869b3050c156055--
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