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 - 03:00:02 PST
