[gmx-users] proton proton transfer

[Ran Friedman]

Sorry for the typo below. DFT based *or* semi empirical code.
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From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Ran Friedman
Sent: 02 December 2010 15:01
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] proton proton transfer

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

------------------------------------------------
Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se
http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en
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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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