Hello Pratul,
thank you too! I have already started reading the EVB manual.
Can this approach also be applied to the system containing transition
metals (like copper) provided the proper parameters are available?
All the best,
Nick
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 05 2019 - 05:30:02 PDT
