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
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