Aside from interacting with solvent-dissolved protons (if you add them), the protonation states are permanent in GMX. All forcefields used in these simulators are non-reactive (beyond vdw and electrostatics).
Unless you run your simulation in stages, where you manually change protonation states, nothing chanes. Alex B> Dear All, B> B> By H++ and reduce we can have the input PDB for pdb2gmx have the B> initial corrected protonated states for some residues, for example, B> HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein B> conformation, the protonated states of the above residues can be changed. B> B> Will you please introduce to me how GROMACS deal with the possible B> protonation state change during the MD process? B> B> Brett -- 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-requ...@gromacs.org.
