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

Albert Sun albert_sun9 at yahoo.com
Tue Nov 4 02:18:01 CET 2003

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.
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.

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...



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