From: somedatta pal (somedatta.pal_at_gmail.com)
Date: Wed Mar 20 2013 - 00:37:21 CDT
Hi,
Thanx for your reply. Without PME, if I use a cutoff value, then
vdw and electrostatic interactions will be calculated within this
distance for all the atoms. But I want to turn off the protein-water
electrostatic interaction completely. Other interactions, like
protein-water vdw
interactions, protein-protein (elect+vdw) interactions, water-water
(elect+vdw) interactions
should be intact. Is their any option in NAMD for performing
simulation in such a way?
I am looking forward for your kind reply.
On 3/19/13, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
> 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
>
>
-- Somedatta Pal
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