[gmx-users] Water density

[Viswanadham Sridhara]

This paper gives lot of information dealing with SPC and other water models.
Hope it helps you.
David van der Spoel, Paul J. van Maaren and Herman J.C. Berendsen
A systematic study of water models for molecular simulation: Derivation of
water models optimized for use with a reaction field.
J Chem Phys 108 pp. 10220-10230 (1998)



On 2/20/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Naser, Md Abu wrote:
> > Thanks david for reply. I have been trying to fix density of a water
> > box at 300k temp. At first I scaled  the density of spc216.gro using
> > editconf and then I have created spc water box using genbox and scaled
> > the water box using editconf -density 1000.  Finally I allowed
> > some vacuum in z direction using editconf again and run for a short
> > time( 2ns) under no pressure and checked using g_density which giving
> > me less density than what I start off. Is it because of vaccum?
> Of course. Same number of waters, larger volume. Run with NPT to test
> the density. Compare to literature.
> >
> > regards,
> > Abu Naser
> > School Of Life Sciences
> > Heriot-Watt University
> > Edinburgh EH14 4AS
> > Email: mn2 at hw.ac.uk <mailto:mn2 at hw.ac.uk>
> > Phone: +44(0)1314518265
> > Fax : +44(0) 131 451 3009
> >
> >
> > ------------------------------------------------------------------------
> > *From:* gmx-users-bounces at gromacs.org on behalf of David van der Spoel
> > *Sent:* Mon 20/02/2006 2:02 PM
> > *To:* Discussion list for GROMACS users
> > *Subject:* Re: [gmx-users] Water density
> >
> > Naser, Md Abu wrote:
> > > Hi All,
> > >
> > > When I run a water box after fixing its density(1kg/L) using editconf,
> > > the density of the box always is going down to 955gm/L. I have been
> > > wondering why this is happening. Can anyone give some clue?
> > >
> > details please.
> >
> > > Abu Naser
> > >
> > > School Of Life Sciences
> > > Heriot-Watt University
> > > Edinburgh EH14 4AS
> > > Email: mn2 at hw.ac.uk
> > > Phone: +44(0)1314518265
> > > Fax : +44(0) 131 451 3009
> > >
> > >
> > >
> > >
> > > Abu Naser
> > >
> > > School Of Life Sciences
> > > Heriot-Watt University
> > > Edinburgh EH14 4AS
> > > Email: mn2 at hw.ac.uk
> > > Phone: +44(0)1314518265
> > > Fax : +44(0) 131 451 3009
> > >
> > >
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
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> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
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>



--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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