[gmx-users] -inter command

João Henriques joao.m.a.henriques at gmail.com
Mon Jan 15 11:51:33 CET 2018

-inter sets the interactive mode for a bunch of other flags. Most are used
for selecting the protonation states of the termini and other residues. It
can also be used for interactive SS bridge selection.

> "for setting the protonation state of charged amino acids in order to
perform simulation at different pH?"

Please note that changing the protonation states of the residues does not
mean you're performing the simulation at a "different pH". A proper
constant-pH MD simulation allows the residues to titrate in respect to the
solution pH as well as the their "molecular environment". In this case,
your residues will be "stuck" in a user defined protonation state that may
or may not reflect the most populated protonation states of those residues
at a given pH, irrespectively of their surroundings.


On Mon, Jan 15, 2018 at 11:00 AM, <zaved at tezu.ernet.in> wrote:

> Dear Gromacs Users
> I have an query regarding gmx pdb2gmx -inter command.
> Do we use -inter command only for setting the protonation state of charged
> amino acids in order to perform simulation at different pH?
> Thank You
> Regards
> Zaved Hazarika
> Research Scholar
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> India
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