[gmx-users] Question regarding box size

James Lord jjamesgreen110 at gmail.com
Fri Jul 10 07:35:24 CEST 2015

Hi all,
I have a system with 300k atoms, but computationally it is expensive for me
doing simulation with such a big system, Is it possible to reduce the box
size? If yes how? (the .gro file is uploaded). I know from Justin tutorial
-nbox        vector 1 1 1
Does the numbers after -nbox have to  integer?

The size of box required to contain protein with 1.5nm of water on each
side. Sorry I could not figure it out what to do and how to tackle this
simple task. re bulding the simulation from scratch is an option but
thought might find quicker and smarter way here. I want to have optimum
size in each direction so that the protein does not see its periodic image.
Appreciate any specific thoughts on my system and the box size I have got



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