NEB with qmmm
ivo6i... at gmail.com
Tue Jun 8 14:14:17 UTC 2010
It was never intended as a lesson. Likely there was some
on my part regarding what was meant by projected band. I thought
band was intended for a NEB calculation in a subspace of collective
like the ones used in metadynamics. A partitioning between active and
degrees of freedom can be done using only positional restraints (not
more complicated colvars). I just didn't realize it wasn't
implemented yet in the
Regarding minimizing the spectator atom, I can imagine systems where
be useful although not in the diglycine system.
On Jun 8, 8:12 am, Teodoro Laino <teodor... at gmail.com> wrote:
> Thanks for the lesson: basically what you are asking for is a minimum
> free energy path, which is at the moment still in a development status -
> Stay tuned if you are interested - cannot guarantee any timeline but
> soon will be released a working version.
> Let me just stress that the possibility to optimize a path in a
> projected subspace has nothing to do with the method you use to compute
> energy and forces (QM, QM/MM or MM).
> Regarding the possibility of free minimizing the rest of the atoms this
> does not make too much sense to me due to the large number of minima
> that you have in a system like gly dipeptide in water.
> ivaylo wrote:
> > They should experience free minimization or free dynamics (depending
> > on
> > which option is chosen) without being influenced by the neighboring
> > replicas.
> > If you had the gly dipeptide in explicit water, surely you wouldn't
> > want to
> > include all the solvent molecules in the band optimization but have
> > them
> > as spectator degrees of freedom. In many cases you wouldn't want to
> > have
> > all the hydrogens in your protein as there may be many motions (such
> > as
> > methyl group rotations) that have nothing to do with the
> > conformational
> > transition of interest.
> > Cheers,
> > --Ivaylo
> > --Ivaylo
> > On Jun 8, 1:46 am, Laino Teodoro <teodor... at gmail.com> wrote:
> >> Ivaylo,
> >> and in your opinion what should happen to all the other atoms which
> >> are not part of the BAND?
> >> Teo
> >> On 8 Jun 2010, at 04:14, ivaylo wrote:
> >>> Hello all,
> >>> I would like to ask if anyone could give me pointers on
> >>> how to use BAND calculations with QMMM in cp2k.
> >>> The regtests in the NEB directory are all classical.
> >>> Specifically, how do you select only a subset of the atoms
> >>> (the QM atoms or ideally a custom subset of the QM atoms)
> >>> to be part of the BAND. Thanks a lot.
> >>> --Ivaylo
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