[gmx-users] setting up a random system

X.Periole X.Periole at rug.nl
Mon Jul 10 06:46:00 CEST 2006

On Mon, 10 Jul 2006 15:13:19 +1200
  "erwin berthier" <erwindownunder at gmail.com> wrote:
> Hello Mark and Jay,
> Thanks for your advice. I see that if I start a system 
>quite less
> dense and let it equilibrate during the run it avoids a 
>lot of
> problems. If I don't do that even the energy 
>minimisation process
> fails. But that seems to work now.
> I thought about removing some particles by hand but is 
>there a program
> that redistributes atom numbers (somehow I don't have 
>the motivation
> for a 100000 atom system)... It would be a pretty easy 
>script to write
> though, but if the tool already exists...

editconf -f toto.gro -o toto-cleaned.gro would give the
right number in the output. Don;t forget to change the
total atom number at the begining of the file.

> About that pressure scaling problem what is the 
>importance of tau_p?
> What does it mean if I change it from 1 to 100 for 
> Cheers,
> Erwin
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