[gmx-users] MD simulation at different pH

Anand Balupuri anandbalupuri.niper at gmail.com
Mon Jun 26 10:03:42 CEST 2017


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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list