On Wed, Apr 3, 2013 at 6:26 AM, Gaurao Dhoke
<g.dhoke.biotec.rwth-aachen.de>wrote:
> Hi,
> Thanks for your reply.
> The question is why I am working with vacuum because I want to know the
> effect of water solvent on protein molecule. So for comparison purpose I am
> doing both 1st in vacuum and then with water.
> If you have any better view about the same please let me know.
>
'effect of water solvent on protein' is an incredibly broad question. Do
you have a more specific question? What solvation effect(s) are you
looking for? As Thomas pointed out, using a force field parametrized to
reproduce behavior in the (polarizing) environment of aqueous solutions is
unlikely to yield appropriate 'vacuum' behavior. Furthermore, you really
do not have experimental results to compare to that I know of, so you won't
be able to 'validate' your vacuum simulation against any experimental
measurements (at least as far as I know -- hopefully someone will fill in
the blanks if I am mistaken).
Since you cannot rely on the vacuum dynamics, you cannot draw meaningful
comparisons between a solvated and unsolvated system.
As a potential counter-example, look at
http://ambermd.org/tutorials/basic/tutorial1/ where a simulation is run in
vacuum of a nucleic acid. Because the strands separate in vacuum (with an
infinite cutoff), you can draw broad conclusions that solvent stabilizes
the association of two DNA strands... but this is a rather contrived
example (i.e., we already knew the answer going in, and it is rather
obvious given the high negative charges on nucleic acids).
My suggestion is to form a more precise question to ask and search the
literature for methods other researchers used to address that question.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 03 2013 - 07:00:08 PDT
