normal How to build and equilibrate a custom sized water box

  • Niels Johan Christensen
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1 year 2 months ago #8136 by Niels Johan Christensen
How to build and equilibrate a custom sized water box was created by Niels Johan Christensen
Dear all.

I was wondering how to create a pre-equilibrated, arbitrarily sized water box.

In the "ht-peptide tutorial" ( cgmartini.nl/index.php/tutorials-general...rial-ht-peptide-gmx5 ) for example, it is mentioned that "...it is recommended to first create an equilibrated water box of that size.".

However, I haven't noticed a description of how to generate such a box anywhere.

Thanks,
Niels

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1 year 2 months ago - 1 year 2 months ago #8137 by bart
Take a look at the lipid tutorial using insane. It is super easy to build an okey initial state for a water box and it will equilibrated within a few minutes on an ordinary desktop.
Last edit: 1 year 2 months ago by bart.

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1 year 2 months ago #8138 by Niels Johan Christensen
Replied by Niels Johan Christensen on topic How to build and equilibrate a custom sized water box

bart wrote: Take a look at the lipid tutorial using insane. It is super easy to build an okey initial state for a water box and it will equilibrated within a few minutes on an ordinary desktop.


Thanks. That worked for me. I used this command to create a water box with side length = 10 nm.
python insane.py -x 10 -y 10 -z 10 -d 0 -pbc cubic -sol W -excl -0.5 -o waterbox_10nm.gro

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