[CP2K:492] Re: Harmonic Potentials

Teodoro Laino teodor... at gmail.com
Thu Dec 20 00:23:47 CET 2007

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,  
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).


> 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
>> 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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