From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 07 2005 - 20:38:26 CDT
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
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).
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
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
Your help will be very much appreciated.
Sorry for bothering all.
--- 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
> 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
> > after solvating the protein, using the following
> > command from autoionize:
> > autoionize -psf file_wb.psf -pdb file_wb.pdb -is
> > -o file_ion
> > I got a warning as follows, even though I tried
> > 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
> > to solve it?
> > 3)I got to know that ion concentration should be
> > the range 1-200 mM, is it correct?
> > Your help will be greatly appreciated.
> > Shirley
> > __________________________________
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