[gmx-users] Simple L-J Particles' simulation

[David]

On Tue, 2003-11-04 at 02:16, Albert Sun wrote:
> Dear Paul.
>  
> 'Randomly produced' meas the coordinates of atoms in x, y, z direction
> are randomly distributed within a cubic box. For example, I generated
> 100 or 10000 atoms randomly distributed in a box with a length of 2
> nm.

the problem is that you can have 1 particle per cubic length unit, not
more. For argon you have dimensionless units (manual ch. 2). 

>  
> My intention is to use L-J particles for simulating a structure with a
> large number of  atoms or grains, which randomly distributed in a box.
>  
> But I met problem and my. gro file does not work. I Checked David's
> files, mdrun is OK.  I don't know what is the problem in my .gro file?
>  
> Many thanks for your time.
>  
> Albert    
>  
> 
> Paul van Maaren <maaren at home.nl> wrote:
>         On Mon, 3 Nov 2003, Albert Sun wrote:
>         
>         > This .gro file is obtained after EM (energy minimization)
>         from a randomly produced .gro file. It did not work when
>         mdrun.
>         
>         What do you mean with randomly produced? Maybe you should
>         start from the 
>         file David send you. If you want 100 atoms, just cut out 25
>         and run mdrun. 
>         That should work. Works for me at least...
>         
>         -- 
>         Groeten,
>         
>         Paul
> 
> 
> ______________________________________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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