[CP2K:2749] Re: NEB with qmmm

Teodoro Laino teodor... at gmail.com
Tue Jun 8 14:12:00 CEST 2010


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
>>>       
>>> --
>>> You received this message because you are subscribed to the Google  
>>> Groups "cp2k" group.
>>> To post to this group, send email to cp... at googlegroups.com.
>>> To unsubscribe from this group, send email to cp2k
>>> +unsub... at googlegroups.com.
>>> For more options, visit this group athttp://groups.google.com/
>>> group/cp2k?hl=en.- Hide quoted text -
>>>       
>> - Show quoted text -
>>     
>
>   




More information about the CP2K-user mailing list