[gmx-users] MD simulation at different pH

[Anand Balupuri]

Dear João,

Thank you for your suggestions.

Regards,
Anand

On Mon, Jun 26, 2017 at 3:47 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> Hi!
>
> You technically can't perform constant-pH simulations with a regular,
> straight out of the box GROMACS distribution. You can change the residue
> protonation states to mimic the "pH" you're interested in simulating, but
> keep in mind that these will be fixed during the entire simulation, i.e.
> there are no (de)protonation events.
>
> For actual constant-pH methods start by reading:
>
> http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
>
> There are other MD simulation packages natively distributed with the
> ability to perform constant-pH simulations (e.g. AMBER).
>
> Best regards,
> João
>
>
> On Mon, Jun 26, 2017 at 3:14 AM, Anand Balupuri <
> anandbalupuri.niper at gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I want to perform MD simulations at different pH using Gromacs 5.0. How
> can
> > I carry out such simulations? Any suggestions?
> >
> > Many thanks,
> > Anand
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