NEB with qmmm

ivaylo ivo6i... at gmail.com
Tue Jun 8 14:03:57 CEST 2010


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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