From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 19 2013 - 01:15:42 CDT
> I want to study how the microscopic stuctural and dynamic properties of water
> molecules present in the vicinity of a protein are expected to be
> sensitive to its local conformational motions and the presence
> of polar and charged groups at the surface capable of anchoring
> water molecules through hydrogen bonds. For this purpose, I performed
> 3 simulations:
> (a) The fully flexible protein molecule
> in equilibrium with the solvent.
> (b) the protein molecule was kept frozen but in equilibrium with solvent.
> (c) The protein molecule was kept frozen and the electrostatic
> interactions between the protein and the water molecules were turned
> In case (c), I made the charge of all the protein atoms zero. Thus
> not only protein-water electrostatic interaction is zero, but also the
> protein-protein electrostatic interactions are also become zero.
> But i want to perform one simulation where protein-water
> interactions (vdw+electrostatic) will be zero, but protein-protein
> interactions remain unchanged.
> I am waiting for your kind reply.
you don't have to repeat what you already wrote. it doesn't make any
difference, since i already *told* you: what you describe is
simulating the protein in vacuum! if there are no protein-water
interactions, then it doesn't matter whether there are water molecules
present at all. case closed.
> Somedatta ..
> I.I.T. Kgp,
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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