[gmx-users] constant protonation state MD

[shahid nayeem]

If I know correctly in lambda dynamics the dynamics of
protonation/deprotonation equilibria is accounted for while my question
relates to the typical constant protonation MD where each titratable group
remains in one protonation state throughout the simulation. Please educate
me
Shahid


On Fri, May 3, 2013 at 6:22 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> I don't have one in mind. It's a delicate question and perhaps I shouldn't
> have phrased it the way I did. Nevertheless, the pKa of most side chains
> mean that their protonation will be dominated by one state for most pH
> values. pKa-shifts and complicated interplay between protonation and
> structure cause exceptions to this and you should be aware that such things
> may in some cases be important. Also consider the timescales of pH-depedent
> structural changes and the length of your simulations. You could check out
> the papers on lambda dynamics by C. Brooks III for an interesting take on
> sampling multiple protonation states.
>
> Best,
>
> Erik
>
> On 3 May 2013, at 14:05, shahid nayeem <msnayeem at gmail.com> wrote:
>
> > Thanks a lot Erik. Could I get some reference based on which you say that
> > much of the structural biology will be largely unaffected.
> >
> > Shahid
> >
> >
> > On Fri, May 3, 2013 at 1:05 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> wrote:
> >
> >> There's no general answer to that. Proton conductivity measurements, for
> >> instance, will be horribly wrong without dynamic protonation. Much (but
> not
> >> all) structural biology, however, will be largely unaffected.
> >>
> >> Erik
> >>
> >> On 3 May 2013, at 04:30, shahid nayeem <msnayeem at gmail.com> wrote:
> >>
> >>> Dear all
> >>>
> >>> Can someone enlighten me on the reliability of the results obtained
> from
> >>> constant protonation state (assigned by different pKa value at
> different
> >>> pH) MD simulation. Also want to know its reliability in case of
> implicit
> >>> solvation model such as PB/GB calculation.
> >>>
> >>> Shahid
> >>> --
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>