[gmx-users] proton proton transfer

[Justin A. Lemkul]

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================