Once again about periodic colvar

Axel akoh... at gmail.com
Thu May 15 16:47:01 UTC 2008

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


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


> 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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