From: somedatta pal (somedatta.pal_at_gmail.com)
Date: Tue Mar 19 2013 - 02:54:35 CDT
---------- Forwarded message ----------
From: somedatta pal <somedatta.pal_at_gmail.com>
Date: Tue, 19 Mar 2013 13:15:15 +0530
Subject: Re: namd-l: Can protein-water interaction be turned off
keeping protein-protein and water-water interactions intact?
To: Axel Kohlmeyer <akohlmey_at_gmail.com>
On 3/19/13, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>> I want to study how the microscopic stuctural and dynamic properties of
>> 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.
I want to study a case when the long-range electrostatic inateraction
between protein and water should be turned off, but short range vdw
interaction between protein and water will be intact. And
protein-protein and water-water interactions (vdw+electrostatic)
should be unchanged. Can you please give any idea, how this can be
>> Somedatta ..
>> I.I.T. Kgp,
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- Somedatta Pal -- Somedatta Pal
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