On Tue, May 10, 2016 at 9:16 AM, Tanmoy Paul <tanmoyp635.gmail.com> wrote:
> Dear Amber users,
> I am trying to perform a series of constant pH
> QM/MM simulations in explicit solvent at different pH. My aim is to carry
> out steered MD to simulate a long range proton transfer reaction at
> different pH where the excess proton hops via GLU and TYR to HIE. Now as
> the reaction is carried out using SMD, I have not changed the residue name
> from GLU to GL4 or HIE to HIP. Instead I have always specified 'ntcnstph'
> value to be equal to nstlim. Is it the right way to do it? Please help.
>
Constant pH does not currently work with QM/MM if you are treating the
titratable residue using a QM Hamiltonian. In particular, constant pH MD
samples the equilibrium distribution of the number of titrating protons, it
does *not* deal with the dynamics of proton transfers at all.
By setting ntcnstph=nstlim, you are effectively running constant
protonation MD (since the protonation states will never try to change
through the constant pH protocol). If you use GLU instead of GL4, you are
not titrating the glutamate residues. So what it seems like you are doing
is exactly equivalent to not using constant pH MD at all.
HTH,
Jason
--
Jason M. Swails
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Received on Tue May 10 2016 - 07:30:04 PDT
