[gmx-users] 2. Proton transfer reaction in gromacs (Padmani Sandhu)

Groenhof, Gerrit ggroenh at gwdg.de
Tue Aug 11 12:55:44 CEST 2015


Since bonds break and form upon proton transfer it requires quantum mechanics, both for the electrons and the proton(s).

To avoid the heavy computational burden,  one can opt to use classical dynamics for the proton and semi-empirical methods, which are accessible in Gromacs (<5) through the QM/MM interface (http://wwwuser.gwdg.de/~ggroenh/qmmm.html),  or EVB, which is not yet available, for the electrons.

Alternatively, if you're happy with only approximately treating the quantum effects of the proton transfer reactions, you can opt for hydyn (DOI: 10.1002/jcc.23536), which allows for proton transfer between water molecules in classical MD simulations. However, it has not been extended to amino acids yet.



   1. Re: Preparation of simulation system for GdmCl and protein
      simulation. (Mark Abraham)
   2. Proton transfer reaction in gromacs (Padmani Sandhu)

Message: 2
Date: Tue, 11 Aug 2015 13:49:41 +0530
From: Padmani Sandhu <padmanisandhu09 at gmail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Proton transfer reaction in gromacs
        <CAKot8D5ju3rVW7-1NoyRhtkbOiX5Xc-urG-_JGqUr1i7Uaw8HQ at mail.gmail.com>
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I want to study proton transfer reaction in a protein channel using
gromacs. I read in the literature that it is not possible to do this by
classical MD, then what are the other ways to perform it in gromacs..??

*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*


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