- Posts: 2
How to build and equilibrate a custom sized water box
- Niels Johan Christensen
- Topic Author
- Offline
- Fresh Boarder
Less
More
4 years 10 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
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
Please Log in or Create an account to join the conversation.
- bart
- Offline
- Admin
Less
More
- Posts: 98
4 years 10 months ago - 4 years 10 months ago #8137
by bart
Replied by bart on topic How to build and equilibrate a custom sized water box
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: 4 years 10 months ago by bart.
Please Log in or Create an account to join the conversation.
- Niels Johan Christensen
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 2
4 years 10 months ago #8138
by Niels Johan Christensen
Thanks. That worked for me. I used this command to create a water box with side length = 10 nm.
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
Please Log in or Create an account to join the conversation.
Time to create page: 0.101 seconds