Harmonic Potentials

Ali RNAlo... at gmail.com
Thu Dec 20 03:04:39 CET 2007


Great. Thanks a million

On Dec 19, 6:23 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> Hi Ali,
>
> On 20 Dec 2007, at 00:15, Ali wrote:
>
>
>
> > Hey Teo,
>
> > Thanks for the push in the right direction. I did see that before but
> > noticed that one has to define a MOLECULE number to use the restraints
> > within COLLECTIVE which in turn requires reading a pdb file (I think).
>
> CONSTRAINT section accepts between the other options: MOLECULE,
> MOLNAME AND
> INTERMOLECULAR (all of them mutually exclusive).
> Now even if you provide an xyz you may ask cp2k to generate a
> topology (but this is yet another
> totally different story..)..
>
> For your case if you want to apply the constraint/restraint without
> even thinking in terms of molecule
> just specify it as intermolecular (in this case the indexes of the
> colvar are global index and not
> any longer indexes connected to the molecule).
>
> ciao,
> teo
>
> > I know I can convert my xyz file into a pdb but I am just curious if
> > there is a way to do it using the xyz file.
>
> > Ali
>
> > On Dec 19, 2:32 am, Teodoro Laino <teodor... at gmail.com> wrote:
> >> Hi Ali,
>
> >> You mean a restraint?
> >> Yes.. First define a COLVAR (BOND in your case) and then use this
> >> COLVAR as a CONSTRAINT/RESTRAINT.
> >> Have a look, as a template, to the several files in cp2k/tests (and
> >> inner directories) grepping for
> >> the &RESTRAINT section.
>
> >> Cheers,
> >> Teo
>
> >> On 19 Dec 2007, at 02:11, Ali wrote:
>
> >>> Dear CP2K Users,
>
> >>> I am currently running and AIMD simulation (no MM system - just QM)
> >>> using a certain basis set and potential.  Is there an easy way to
> >>> add
> >>> in a harmonic potential between specific atoms in my system? Do I
> >>> have
> >>> to define a "molecule" first? This is not a QM/MM system, so I was
> >>> wondering if there was a convenient way to do this?
>
> >>> Ali


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