NEB with qmmm
ivo6i... at gmail.com
Tue Jun 8 14:03:57 CEST 2010
They should experience free minimization or free dynamics (depending
which option is chosen) without being influenced by the neighboring
If you had the gly dipeptide in explicit water, surely you wouldn't
include all the solvent molecules in the band optimization but have
as spectator degrees of freedom. In many cases you wouldn't want to
all the hydrogens in your protein as there may be many motions (such
methyl group rotations) that have nothing to do with the
transition of interest.
On Jun 8, 1:46 am, Laino Teodoro <teodor... at gmail.com> wrote:
> and in your opinion what should happen to all the other atoms which
> are not part of the BAND?
> 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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