[gmx-users] Water density

[Naser, Md Abu]

Hi Viswanadham Sridhara and Michael Patra,

Thank you very much for your reply. I have solved the problem. It was just spc water model which dose not give good estimate of density at room temperature. I am now using spce which is giving correct density even in vacuum.

Thanking you all,


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 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Viswanadham Sridhara
Sent: Mon 20/02/2006 5:11 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Water density
 
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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>
> --
> 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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