Box size by packmol

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1

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hello users
please give me idea or step to how to pack any molecules in packmol and how to calculate how much should be box size?
is there any formula for how much should be box size?

2

Check Packmol website, it has enough info and example .inp files to setup simple to complex systems.

You can get .pdb file from Packmol and then convert it to .gro using VMD. Use gmx editconf with -d option to define distance between protein and box side. How big should be the box? That depends on your studies but at a minimum I suggest atleast 1.5 nm distance between atoms and box side.

3

thanks for reply