I'm using the difference between the (his)N-H(serine) and the O-H distance.
Il giorno 22/nov/2012, alle ore 11:34, Alex Rodriguez <alexdepremia.gmail.com> ha scritto:
> What collective variable/s are u using?
> A.
>
>
> On Wed, Nov 21, 2012 at 4:17 PM, Jacopo Sgrignani <sgrigna.sissa.it> wrote:
>
>>
>> Dear all
>> I'm studying an enzymatic reaction using semi-empirical QM/MM Metadynamics.
>> I'm using amber12 as MD engine and Plumed to enable metadynamics.
>> Unfortunately I have a very big problem.
>> In practice I'm investigating a deprotonation of a serine residue by
>> an hystidine; at the beginning of the simulation the geometry of the
>> system is well described, however after the deprotonation happens the
>> serine residue takes the hydrogen atom bound to one of the carbon
>> atoms of the hystidine ring.
>> I've tried different semiempirical methods as DFTB with 3rd order
>> correction, or PM6, PM6-DH+ but I still have this problem.
>> In the initial phase of my study I had a negatively charged QM part
>> and maybe I could have problems related with electron delocalizations,
>> then I have reduced the QM part and now I have only serine and
>> hystidine (the minimal system to investigate the reaction).
>> Did anybody have the same experience? Do you have advices?
>>
>> Thanks a lot
>>
>> Jacopo
>>
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Received on Thu Nov 22 2012 - 03:00:03 PST
