How to prepare a pdb file of 256 ions pairs in cubic form using genconf command

User discussions
1

GROMACS version:2022.4
GROMACS modification: Yes/No
I have to prepare a pdb file of 256 ions pairs using genconf command. I have facing problem in choosing -nbox value,so that I have a cubic structure of pdb file. How to prepare a cubic structure pdb file of 256 ions pairs.

2

Hi,
I think that gmx genconf is not what you want. Depending on the type of ions and system. you can look to the following tools. For both of them you have to generate a box in advance with the appropriate dimension according to ion concentration you would like to have:
[gmx insert-molecules]
(https://manual.gromacs.org/current/onlinehelp/gmx-insert-molecules.html#gmx-insert-molecules)
gmx genion
\Alessandra

3

Thankyou,I will try this.
Actually, I want to replicate the system upto 256 ions pairs.