From: somedatta pal (somedatta.pal_at_gmail.com)
Date: Thu Mar 21 2013 - 23:49:13 CDT
Dear Sir,
I am not an expert for modifying the source code. Can you
please help me
in this matter by sending the modified source code ?
Regards,
Somedatta.
On 3/20/13, Grace Brannigan <grace.brannigan_at_rutgers.edu> wrote:
> Hi Somedatta,
>
> I could be wrong, but I think this should be possible using the Alchemical
> FEP tool. Usually this tool is used to gradually turn off interactions
> between a ligand and a protein, using a coupling parameter lambda, but you
> could just do the simulation using one value of the coupling parameter
> which corresponded to the interactions you wanted. You can turn off VDW and
> electrostatics separately using this tool. Then, of course, your "ligand"
> would be all of the waters in the system ; the developers could tell you
> whether it would be computationally prohibitive.
>
> In any case, if you are looking to modify the code, my guess is that much
> of the work is already done as part of the FEP module, and may just need
> slight tweaks.
>
> cheers,
> Grace
>
>
>
>
> On Wed, Mar 20, 2013 at 3:47 AM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> I guess there's currently no way how to do that with namd. You would have
>> to
>> implement it by yourself. Additionally, you could just compute the
>> electrostatic potential instead of sampling over varying configurations
>> to
>> see what's happening, or?
>>
>> 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: Mittwoch, 20. März 2013 06:37
>> > An: Norman Geist; namd-l
>> > Betreff: Re: namd-l: Can protein-water electrostatic interaction be
>> > turned off keeping protein-protein (vdw+elect) and water-water
>> > (vdw+elect) interactions intact?
>> >
>> > 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
>>
>>
>>
>
>
> --
> Grace Brannigan, Ph.D.
> Assistant Professor
> Center for Computational and Integrative Biology (CCIB) &
> Department of Physics
> Rutgers University, Camden, NJ
> (856)225-6780
> www.branniganlab.org
>
-- Somedatta Pal
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