[gmx-users] density of zinc

[David]

On Tue, 2005-08-02 at 09:15 -0700, Budiono wrote:
> Hi all.
>  
> I am trying to simulate interactions between solid walls and solvents.
> First, i made model for solid and i used zinc as the material and i
> used ffgmx Gromacs forcefield because i found the zinc residue
> in ffgmx.rtp file
>  
> then when i calculated the density of zinc using g_density , i got
> somewhat strange result : 
>               box (nm)          density (kg/m3)
>                                   0
>                                   0
>                            0.371568
>                                   0
>                            0.743136
>                             317.403
>                              1.1147
>                             486.683
>                             1.48627
>                             550.164
>                             1.85784
>                             550.164
>                             2.22941
>                             486.683
>                             2.60098
>                             317.403
>                             2.97254
>                                   0
>                             3.34411
>                                   0
> 
> as i know the density of zinc is around 7000 kg/m3, isn't it ?? i used
> "freezegrps" options.
> 
> so, does anyone know how to deal with this problem ???
Do you have a solid piece of Zn? If your starting coordinates are OK
then the density should be OK. But don't expect a simple force field
model to be great for Zn, unless you model it as a Lennard-Jones
particle.
> 
> thanks a lot
> 
> Budiono  
> 
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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://xray.bmc.uu.se/~spoel
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