[gmx-users] Water density

[David van der Spoel]

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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-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++