[gmx-users] proton proton transfer

[Ran Friedman]

Hi Olga,

It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. 

Ran 

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Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
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________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Olga Ivchenko [olga.ivchenko at gmail.com]
Sent: 02 December 2010 14:59
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] proton proton transfer

Thnaks, Justin.
Probably CHARMM is suitable for this.

2010/12/2 Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>>


Olga Ivchenko wrote:
Dear gromacs users,

I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs.
I read about umbrella sampling, but may be there is other techniques?


You can't do this with standard MD.  Bonds cannot break and re-form in a classical force field.  You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs.

-Justin

Yours sincerely,
Olga


--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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