[gmx-users] constant protonation state MD

[Erik Marklund]

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