[gmx-users] Water density
Naser, Md Abu
mn2 at hw.ac.uk
Mon Feb 20 20:07:13 CET 2006
Thank you very much for yor pointing out possible sources of artifacts and advise. I will look at the paper.
School Of Life Sciences
Edinburgh EH14 4AS
Email: mn2 at hw.ac.uk
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 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 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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