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

[David van der Spoel]

On Sat, 8 Nov 2003, Albert Sun wrote:

>Hi, David, 
>I could not understand why I can ONLY have 1 particle per cubic length unit, not
>more?
vanderwaals radius is 1
>Thanks!
> 
>
>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.
>________________________________________________________________________
>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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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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