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

Albert Sun albert_sun9 at yahoo.com
Sat Nov 8 20:31:02 CET 2003

Hi, David, 
I could not understand why I can ONLY have 1 particle per cubic length unit, not

David <spoel at xray.bmc.uu.se> wrote:
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 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 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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