On Sun, 26 Mar 2017 22:02:04 +0200
Szymon Żaczek <szymonzaczek.gmail.com> wrote:
> Dear Amber Mailing List,
>
> I'm trying to estimate the free energy barrier of SN2 reaction in
> solution using thermodynamic integration approach implemented within
> sander, where bromine is substituted by iodine in 2-bromoethylbenzene.
>
> Topology files were created in such a manner, that 2-bromoethylbenzene
> and the unbound iodine placed in the close vicinity of the rest of the
> system were solvated using standard tleap procedure (20 Å box). Then,
> the first prmtop file was saved. Next, the bond between carbon and
> bromine was deleted and replaced by a bond between carbon and iodine,
> what somehow describes the reaction.
I am not entirely sure how that should work. When you delete bonds
then that means that your halogens can freely drift within the
simulation box. Within a QM/MM context what does an intermediate
clambda mean? TI is defined within the context of thermodynamic
cycles. So what is the cycle you have in mind?
Cheers,
Hannes.
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Received on Tue Mar 28 2017 - 06:30:03 PDT
