[gmx-users] Water density

[Naser, Md Abu]

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? 
 
regards,
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 
  

________________________________

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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