If the goal is to model proton transfer, an alternative to consider is Empirical Valence Bond (EVB) model available in AMBER. It is based on classical force-field (with Morse potential representations for the transferring proton) so it is much faster than QM/MM. You can include solvent and consider multiple states/reactions.
But obviously it really depends on what you are trying to investigate, EVB may not fit your needs.
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 6/4/2019 8:45 AM, Nikolay N. Kuzmich wrote:
Hello David,
thank you for the answer.
Yes, taking into account the solvent effects here may be really challenging
- I guess I need to read through the literature on the matter.
The thoughts for right now are either to consider a continuum model or
make it QM/MM simulation with the waters of interest in QM part and to
include remaining explicit waters in the MM part as 3- or 4-point model...
Kind regards,
Nick
On Mon, Jun 03, 2019, Nikolay N. Kuzmich wrote:
I would like to ask you if it is possible to perform
quantum-mechanical simulations of a proton transfer in Amber.
Is this tutorial about it?
ambermd.org/tutorials/advanced/tutorial10/index.html
Using DFTB, for instance.
That tutorial is indeed about simluations of the thermodynamics of
proton transfer, using the DFTB Hamiltonian. Note that this is just a
"how-to" to perform a certain type of simulation--as far as I can see,
it draws no conclusions about the accuracy of the results (vis-a-vis the
real physical system.) Also note that thsi is a "vacuum" tutorial:
carrying out such simulations in a protic solvent like water would
probably be much more challenging.
...regards..dac
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Received on Tue Jun 04 2019 - 06:30:02 PDT
