Re: [AMBER] EVB calculations of proton transfer

From: kenfack cyril <>
Date: Mon, 1 Aug 2016 21:05:09 +0000 (UTC)

Thank  for your replyThe solvent is not directly involved in the proton transfer process, i mean is neither donor nor acceptor, but just create a barrier by H-bonding that is opposed to the proton transfer reaction. The proton transfer itself  is intramolecular.
This problem can be handle by EVB calulations, our results are encouragingbut we would like to have some helping hand.
Best regardsCyril
 Dr. KENFACK ASSONGO Cyril Centre for Atomic Molecular Physics and Quantum Optics (CEPAMOQ) Faculty of Science - University of Douala P.O. Box 8580 Douala - CAMEROON Tel. actuel : 0023796031051 Fax: 237) 3343 46 08 Email:

    On Monday, August 1, 2016 3:52 PM, David A Case <> wrote:

 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.


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Received on Mon Aug 01 2016 - 14:30:02 PDT
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