From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 19 2013 - 10:18:35 CDT
Hi,
without PME you will have turned off long range electrostatics. Now you can
control the range of vdw and short range electrostatics by changing the
cutoff value.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von somedatta pal
> Gesendet: Dienstag, 19. März 2013 08:55
> An: namd-l
> Betreff: Fwd: namd-l: Can protein-water interaction be turned off
> keeping protein-protein and water-water interactions intact?
>
> ---------- 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:
> >> Hi,
> >> 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
> >> off.
> >> 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.
> >
> > axel.
> >
>
> Hi,
>
> 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
> done?
> >
> >
> >>
> >> Somedatta ..
> >> I.I.T. Kgp,
> >> India
> >
> >
> >
> > --
> > 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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