On Sat, Jul 30, 2016, kenfack cyril wrote:
> I'm working on proton transfer reaction using the evb model ...
> I would like to simulate the proton transfer kinetic in different media
> such as protic or aprotic solvent could some one help me with input
> file to adapt to my on work, or a protocol for performing MD with two
> states in the EVB model framework.
I think you need to be more specific in your question. Is the protic
solvent directly involved in the proton transfer event? (That is, is there
an intermediate that involves proton transfer to or from a solvent molecule?)
That sort of calculation is not directly supported in Amber, although what is
there might form a useful foundation for code extensions.
If the solvent is "innocent" (just providing a background environment),
then you handle it in the same way as you would for non-EVB calcualtions.
In practice, one should always simulate the starting and ending states
with non-EVB calcualtions first (to make sure you are happy with the
results,) before tackling the transfer problem.
...dac
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Received on Mon Aug 01 2016 - 08:00:05 PDT
