[gmx-users] constant protonation state MD

[Erik Marklund]

Yes that's what lambda dynamics does. I mentioned it since it addresses the interplay between protonation and structure. So to answer your original question: it depends.

Erik

On 3 May 2013, at 15:27, shahid nayeem <msnayeem at gmail.com> wrote:

> 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
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