[gmx-users] Water density

[Naser, Md Abu]

Hi David,

Thank you very much for yor pointing out possible sources of artifacts and advise. I will look at the paper.

With 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 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Mon 20/02/2006 7:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Water density
 
Naser, Md Abu wrote:
>
> 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,
>
It's not as easy as that. Much depends on simulation conditions, for
instance the DispCorr = EnerPres also yields a density increase of 12-15
g/l. A larger cut-off gives higher density, reaction field lower
density. Please do also check:

David van der Spoel and Paul J. van Maaren: /The origin of layer
structure artifacts in simulation of liquid water/ J. Chem. Theor. Comp.
*2* pp. 1-11 (*2006*)

Not just to plug my own work, but because this stuff is not
straight-forward and you may get counter-intuitive results if you play
with the parameters without carefully checking the result. It is alway
good practice to try to reproduce results from the literature!

-- 
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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