[gmx-users] Water density
muta.mestri at gmail.com
Mon Feb 20 22:10:50 CET 2006
Is the paper[(David van der Spoel and Paul J. van Maaren: /The origin of
structure artifacts in simulation of liquid water/ J. Chem. Theor. Comp.
*2* pp. 1-11 (*2006*)) ]already published and available online?
I tried to find it, but I could not get it.
If possible, can you forward that to the Discussion List?
Thanks a lot,
On 2/20/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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 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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Graduate Research Assistant,
Old Dominion University, "VIRGINIA".
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