LJ to semi-empirical

[Axel]

ivan,

On Sep 17, 7:15 am, ivan <solt... at yahoo.com> wrote:
> Hi Axel,
>
> thanks for your help. i would prefer a pure semi-empirical simulation,

that is understandable, but as juerg pointed out, without
support for periodic boundary conditions, you can do only
cluster calculations.

> rather than a hybrid run. it's not clear to me if AM1 or PM3 can be
> used with some kind of stochastic boundary conditions (or anything
> else, that simulates a thermostat), or not. Are they only suitable for

i don't quite get what you mean with 'simulate a thermostat'.
the way i understand juergs post is, that cp2k currently does not
account for the interactions between periodic images. you can use
thermostat just fine, but with a cluster calculation the problem is
how to control the density etc.
hence my suggestion for doing a qm/mm calculation. this would
give you almost ideal boundary conditions for the SE cluster.
and for that i'd have a couple more ideas on how you'd get
the optimal correction to the interactions with minimal additional
programming by mostly using features already present in cp2k.

cheers,
    axel.

> gas-phase calculations at present stage?
>
> regards
> ivan
>
> On szept. 13, 18:16, Axel <akoh... at gmail.com> wrote:
>
> > hi ivan,
>
> > how about just taking a large classical TIP3P water box
> > and doing a QM/MM run with a large AM1 box/cluster in it?
> > thanks to teo's recent efforts SE-QM/MM seems to be
> > working fine now. that may not get you all the way, but
> > i am certain that it would still be worth investigating it.
> > please contact me at akoh... at cmm.chem.upenn.edu, if you
> > want to discuss in more detail.
>
> > cheers,
> >    axel.
>
> > On Sep 13, 6:54 am, ivan <solt... at yahoo.com> wrote:
>
> > > Hi Teo and Juerg
>
> > > thanks for the quick reply. Actually, i'm absolutely new at CP2K (i've
> > > downloaded the code only a few days ago), so i don't have a working
> > > input yet. If i can't create it pretty soon, i will show up here
> > > again.. This option sounds great
> > > for me, but if (as Juerg warned me in his meassage) AM1 can not be
> > > used with a periodic boundary, i'm a little lost again. Thanks anyway
>
> > > regards
> > > ivan
>
> > > On szept. 13, 12:43, Juerg Hutter <hut... at pci.uzh.ch> wrote:
>
> > > > Hi
>
> > > > I just wanted to add that currently periodic boundary
> > > > conditions cannot be used with the NDDO (AM1, PM3 etc)
> > > > models in cp2k.
>
> > > > regards
>
> > > > Juerg
>
> > > > ----------------------------------------------------------
> > > > Juerg Hutter                   Phone : ++41 44 635 4491
> > > > Physical Chemistry Institute   FAX   : ++41 44 635 6838
> > > > University of Zurich           E-mail: hut... at pci.uzh.ch
> > > > Winterthurerstrasse 190
> > > > CH-8057 Zurich, Switzerland
> > > > ----------------------------------------------------------
>
> > > > On Thu, 13 Sep 2007, ivan wrote:
>
> > > > > Dear All,
>
> > > > > i am trying to reproduce the diffusivity (and g(r)) of a classical
> > > > > water model (TIP3P) with semi-empirical water (probably AM1, might be
> > > > > PM3). For this aim, i would like to add an artificially tuned Lennard-
> > > > > Jones term to the AM1 energy. Where do you think i should touch the
> > > > > cp2k code to do that? Many thanks in advance for any idea
>
> > > > > regards
> > > > > ivan