[gmx-users] proton proton transfer

[Olga Ivchenko]

Thnaks, Justin.
Probably CHARMM is suitable for this.

2010/12/2 Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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