Hi Shahid,
As Erik said, it depends... on your system, on the process you are
studying in that system, on the property you think it's relevant to study
that process, etc.
If your question refers to the (de)protonation of acidic and basic groups
usually occuring in aqueous solution, there are methods to perform what is
called constant-pH MD, where the protonation states of those groups change
in a discrete or continuous way along the simulation. If you are
interested, start with the corresponding GROMACS how-to
(http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation) and
then search the literature.
In any case, you don't need any of that fancy stuff unless you have
reasons to think that the properties you want to study in your system are
strongly dependent on protonation-conformation coupling effects. In some
cases you may be suspicious about the effect of the protonation state of
one group (e.g., a histidine), but that can be simply tested by performing
two constant-protonation MD simulations, one for each state (you can even
try to use a linear response approximation on top of that). But in most
cases you don't need even that.
For what it's worth: I was one of the first to develop and apply
constant-pH MD and I don't bother to use it most of the time... :)
Best,
Antonio
On Fri, 3 May 2013, Erik Marklund wrote:
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 <msnay...@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 <er...@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 <msnay...@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 <er...@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 <msnay...@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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Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619 email: bapti...@itqb.unl.pt
fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista
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