[CP2K:2751] Re: NEB with qmmm

Teodoro Laino teodor... at gmail.com
Tue Jun 8 16:19:44 CEST 2010


At the moment I'm thinking only to implement a projection in a subspace 
of CV.
One can always define X,Y,Z as CV and retrieve what you are looking for.

It is not fully clear to me what you intend with
"[..] only putting positional restraints [..]"

but it is clear that if you put positional restraints (to the set of 
atoms that you call spectators) you will never get a minimum FES - 
rather just 1 point in a multidimensional FES.
Kind of umbrella sampling in a trajectory space - That's will not be 
available.

Cheers
Teo

ivaylo wrote:
> It was never intended as a lesson. Likely there was some
> misunderstanding
> on my part regarding what was meant by projected band. I thought
> projected
> band was intended for a NEB calculation in a subspace of collective
> variables
> like the ones used in metadynamics. A partitioning between active and
> spectator
> degrees of freedom can be done using only positional restraints (not
> necessarily
> more complicated colvars).  I just didn't realize it wasn't
> implemented yet in the
> regular NEB.
>
> Regarding minimizing the spectator atom, I can imagine systems where
> it could
> be useful although not in the diglycine system.
>
> --Ivaylo
>
> On Jun 8, 8:12 am, Teodoro Laino <teodor... at gmail.com> wrote:
>   
>> Thanks for the lesson: basically what you are asking for is a minimum
>> free energy path,  which is at the moment still in a development status -
>> Stay tuned if you are interested - cannot guarantee any timeline but
>> soon will be released a working version.
>>
>> Let me just stress that the possibility to optimize a path in a
>> projected subspace has nothing to do with the method you use to compute
>> energy and forces (QM, QM/MM or MM).
>>
>> Regarding the possibility of free minimizing the rest of the atoms this
>> does not make too much sense to me due to the large number of minima
>> that you have in a system like gly dipeptide in water.
>>
>> Teo
>>
>>
>>
>> ivaylo wrote:
>>     
>>> 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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>> - Show quoted text -
>>     
>
>   




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