[gmx-users] constant protonation state MD

[Erik Marklund]

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
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