From: Shirley Li (li19104_at_yahoo.com)
Date: Mon Oct 10 2005 - 18:05:34 CDT
Thank JC a lot for the great help and information.
Shirley
--- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> 1) If you plan to use periodic boundary conditions
> (which I believe is the
> case here), then you ONLY need a water box. The
> water sphere is for
> non-periodic conditions.
>
> 2) After you finish building your system (solvating,
> ionizing, etc.), you
> should do some minimization. Also, depending on
> your system, you might want
> to equilibrate with protein backbone restrained,
> then unrestrained.
> Properly setting up your system will take a little
> trial and error on your
> part, but be sure to watch its behavior to make sure
> it doesn't do anything
> you don't
want early on (e.g. water entering a
> cavity that should be closed
> off to it).
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Shirley Li
> Sent: Friday, October 07, 2005 9:50 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: water box and the procedure
>
> Thank JC so much for the kind help. I'm working on
> my
> system by following the NAMD tutorial, and I have
> some
> further questions as follows:
>
> 1) Regarding the step of adding/equilibrating water
> sphere and that of water box (wbox), it seems that
> they are completely independent. The step of
> adding/equilibrating water box does NOT take any
> information(input) from the result of water sphere,
> is
> this correct? If so, is the purpose of adding water
> sphere only to check if the box size is big enough?
>
> 2) From the tutorial, it seems to me that it starts
> the equilibration run immediately after finishing
> adding water box (probably I misunderstood this
> part). I wonder if one should do the following: a)
> minimize wbox; b) equilibrate wbox; c) heat the
> entire system; d) eq the entire system; e)
> restrained
> MD; f) free MD? If so, are there scripts for all of
> these steps?
>
> Your help will be very much appreciated.
>
> Sorry for bothering all.
>
> Shirley
>
>
>
>
> --- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
> > 1) After. Autoionize chooses the positions of the
> > ions based on water
> > molecules (it removes a water molecule for each
> ion
> > placed).
> >
> > 2) Autoionize is trying to satisfy two
> constraints:
> > neutralizing the
> > system and matching the desired concentration.
> > However, if your system
> > size is small, it only requires a few ions to
> match
> > the concentration.
> > But your charge is so large that it requires a lot
> > of Na+ just to
> > neutralize it! Unfortunately, you only have two
> > courses of action:
> > increasing your concentration until you get a mix
> of
> > charges (but
> > possibly going beyond physiological conditions) or
> > increasing your
> > system size. Although, I think, for most purposes
> > you won't really
> > need the chloride ions unless you know they are
> > important to the
> > function of what you are studying.
> >
> > 3) I'm not a biologist by training, so I can't say
> > with certainty, but
> > that range seems reasonable (I think I've seen in
> > the literature
> > 100-150 mM before).
> >
> >
> > On Oct 6, 2005, at 6:36 PM, Shirley Li wrote:
> >
> > > Thanks a lot.
> > >
> > > I have some further THREE questions:
> > >
> > > 1) Should ions be added AFTER or BEFORE the
> > protein is
> > > solvated?
> > >
> > > 2) The protein is -36e charged. I tried to add
> > ions
> > > after solvating the protein, using the following
> > > command from autoionize:
> > > autoionize -psf file_wb.psf -pdb file_wb.pdb -is
> > 0.05
> > > -o file_ion
> > >
> > > I got a warning as follows, even though I tried
> > "-is
> > > 0.2":
> > >
> > > WARNING: ion concentration too low, cannot add
> Cl
> > > ions!
> > > Adding 36 Na and 0 Cl ions, total 36 ions
> > >
> > > Could sb tell me this is an important issue, and
> > how
> > > to solve it?
> > >
> > > 3)I got to know that ion concentration should be
> > in
> > > the range 1-200 mM, is it correct?
> > >
> > > Your help will be greatly appreciated.
> > >
> > > Shirley
> > >
> > >
> > >
> > > __________________________________
> > > Yahoo! Mail - PC Magazine Editors' Choice 2005
> > > http://mail.yahoo.com
> >
> >
>
>
>
>
>
>
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