How do I generate PSF ?

Axel akoh... at
Mon Jan 21 15:42:26 UTC 2008

On Jan 21, 2:06 pm, "Jack Shultz" <jackyg... at> wrote:
> My goal is to learn how to design a covalent bond-breaking reaction model.
> So I do what usually works for me with most applications, take an example I
> know works 2gly_CI-NEB.inp but I try to build the inital and final images
> using H2O2, H2O & O2 molecular files. I modified these files.
> I only want the final geometry to represent two water molecules and one
> diatomic oxygen with sufficient distance to make any weak interactions such
> as hydrogen bonds non-existent So I've displaced them 2 angstroms along x
> and now I tried 1 angstrom along y.
> So I guess I can use that triangle formula since it is only two axis. 2sqr +
> 1sqr = csqr = 5 so c = sqrt 5 < 2.8 ... maybe not enough distance.
> As far as the FF goes, can you point me to an example that has FF configured
> correctly for a bond-breaking reaction? Moreover, are there any

almost all traditional classical (pairwise additive) force fields do
not support bond breaking.

if you want to look at bond breaking, why not use semi-empirical
or DFT? then you don't need to provide topology information.

in the danger of repeating myself. please go an _first_ study a bit
on how the various modeling methods work, what they can do and
don't try to do too many things at the same time (NEB is really very
much at the end of this 'food chain'). it will pay off in time, and
don't have to ask about things, that puzzle you now, but are
essentially trivial.


> bond-breaking examples I can look at?
> Jack
> On Jan 21, 2008 2:58 AM, Teodoro Laino <teodor... at> wrote:
> >  On 21 Jan 2008, at 04:35, Jack Shultz wrote:
> > So I did not displace the water molecules appropriately?
> > what do you mean with appropriately? If that is the geometry that you want
> > to get as your final state.. that's fine.. but don't expect
> > the topology generator to work properly with it..
> > I only tried to seperate them by 2 angstroms along the x-axis...maybe I
> > should move them 1 angstrom along the y-axis as well?
> > a typical hydrogen bond (O1-O2) for bulk water is ~ 2.8 angstrom..  (as
> > you said yours is 2.0 Angstgrom)..
> > Should that help?
> > Sorry.. I don't understand why/where you are expecting an help changing
> > the geometry of the final state of the NEB.
> > Perhaps, I was not clear in my last message:
> > You've setup a bond-breaking reaction with a classical FF: 1) You didn't
> > provide any parameter file for the classical FF (!) (and this causes the
> > abnormal termination of cp2k)
> > 2) You cannot do BB* with CP2K, using a classical Hamiltonian.
> > *(Bond-Breaking)
> > cheers,
> > Teo

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