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<P><FONT SIZE=2>Hi Viswanadham Sridhara and Michael Patra,<BR>
<BR>
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.<BR>
<BR>
Thanking you all,<BR>
<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Viswanadham Sridhara<BR>
Sent: Mon 20/02/2006 5:11 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] Water density<BR>
<BR>
This paper gives lot of information dealing with SPC and other water models.<BR>
Hope it helps you.<BR>
David van der Spoel, Paul J. van Maaren and Herman J.C. Berendsen<BR>
A systematic study of water models for molecular simulation: Derivation of<BR>
water models optimized for use with a reaction field.<BR>
J Chem Phys 108 pp. 10220-10230 (1998)<BR>
<BR>
<BR>
<BR>
On 2/20/06, David van der Spoel <spoel@xray.bmc.uu.se> wrote:<BR>
><BR>
> Naser, Md Abu wrote:<BR>
> > Thanks david for reply. I have been trying to fix density of a water<BR>
> > box at 300k temp. At first I scaled the density of spc216.gro using<BR>
> > editconf and then I have created spc water box using genbox and scaled<BR>
> > the water box using editconf -density 1000. Finally I allowed<BR>
> > some vacuum in z direction using editconf again and run for a short<BR>
> > time( 2ns) under no pressure and checked using g_density which giving<BR>
> > me less density than what I start off. Is it because of vaccum?<BR>
> Of course. Same number of waters, larger volume. Run with NPT to test<BR>
> the density. Compare to literature.<BR>
> ><BR>
> > regards,<BR>
> > Abu Naser<BR>
> > School Of Life Sciences<BR>
> > Heriot-Watt University<BR>
> > Edinburgh EH14 4AS<BR>
> > Email: mn2@hw.ac.uk <<A HREF="mailto:mn2@hw.ac.uk">mailto:mn2@hw.ac.uk</A>><BR>
> > Phone: +44(0)1314518265<BR>
> > Fax : +44(0) 131 451 3009<BR>
> ><BR>
> ><BR>
> > ------------------------------------------------------------------------<BR>
> > *From:* gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
> > *Sent:* Mon 20/02/2006 2:02 PM<BR>
> > *To:* Discussion list for GROMACS users<BR>
> > *Subject:* Re: [gmx-users] Water density<BR>
> ><BR>
> > Naser, Md Abu wrote:<BR>
> > > Hi All,<BR>
> > ><BR>
> > > When I run a water box after fixing its density(1kg/L) using editconf,<BR>
> > > the density of the box always is going down to 955gm/L. I have been<BR>
> > > wondering why this is happening. Can anyone give some clue?<BR>
> > ><BR>
> > details please.<BR>
> ><BR>
> > > Abu Naser<BR>
> > ><BR>
> > > School Of Life Sciences<BR>
> > > Heriot-Watt University<BR>
> > > Edinburgh EH14 4AS<BR>
> > > Email: mn2@hw.ac.uk<BR>
> > > Phone: +44(0)1314518265<BR>
> > > Fax : +44(0) 131 451 3009<BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > > Abu Naser<BR>
> > ><BR>
> > > School Of Life Sciences<BR>
> > > Heriot-Watt University<BR>
> > > Edinburgh EH14 4AS<BR>
> > > Email: mn2@hw.ac.uk<BR>
> > > Phone: +44(0)1314518265<BR>
> > > Fax : +44(0) 131 451 3009<BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > ><BR>
> > ><BR>
> ------------------------------------------------------------------------<BR>
> > ><BR>
> > > _______________________________________________<BR>
> > > gmx-users mailing list gmx-users@gromacs.org<BR>
> > > <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
> > > Please don't post (un)subscribe requests to the list. Use the<BR>
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> ><BR>
> ><BR>
> > --<BR>
> > David.<BR>
> > ________________________________________________________________________<BR>
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
> > Dept. of Cell and Molecular Biology, Uppsala University.<BR>
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
> > phone: 46 18 471 4205 fax: 46 18 511 755<BR>
> > spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>
> > _______________________________________________<BR>
> > gmx-users mailing list gmx-users@gromacs.org<BR>
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> > Please don't post (un)subscribe requests to the list. Use the<BR>
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> ><BR>
> > ------------------------------------------------------------------------<BR>
> ><BR>
> > _______________________________________________<BR>
> > gmx-users mailing list gmx-users@gromacs.org<BR>
> > <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
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><BR>
><BR>
> --<BR>
> David.<BR>
> ________________________________________________________________________<BR>
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
> Dept. of Cell and Molecular Biology, Uppsala University.<BR>
> Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
> phone: 46 18 471 4205 fax: 46 18 511 755<BR>
> spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>
><BR>
><BR>
> _______________________________________________<BR>
> gmx-users mailing list gmx-users@gromacs.org<BR>
> <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
> Please don't post (un)subscribe requests to the list. Use the<BR>
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> Can't post? Read <A HREF="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR>
><BR>
<BR>
<BR>
<BR>
--<BR>
Viswanadham Sridhara,<BR>
Graduate Research Assistant,<BR>
Old Dominion University, "VIRGINIA".<BR>
<BR>
<BR>
</FONT>
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