Once again about periodic colvar

ilya ily... at gmail.com
Fri May 16 06:33:01 UTC 2008

Well, I mean that rotation begins independently of gaussian params
when the filled depth of the potential well is no more than 1 kcal/mol
(but should be about 7 for butane rotation).
I thought about what is called "hill surfing" but after more
experiments I don't think that it is the source of such behavior (I've
tried small hills and large stride).


On May 15, 8:47 pm, Axel <akoh... at gmail.com> wrote:
> On May 15, 10:13 am, ilya <ily... at gmail.com> wrote:
> > Hello!
> > Well, I performed another test reaction which is Cl- + CH3Cl (from the
> > article).
> > I have successfully build a 3d fes which is very similar to that one
> > in the article and I think I've got the idea of choosing parameters
> > for metadynamics.
> >    BUT
> > For the case of butane I can't obtain any adequate free energy
> > profile.
> > I observed that after some point  the molecule starts spinning
> > strangely around C2-C3 bond and I think the are still some bugs in the
> ilya,
> please describe "strangely".
> once you have filled all minima
> with gaussians you are supposed to
> have the molecule rotating freely
> around the C2-C3 bond (no more barrier
> left!).
> cheers,
>     axel.
> > case of periodic colvar in code.
> > Maybe someone else with more experience in metadynamics would also try
> > to do this? Maybe I am doing something wrong?

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