[gmx-users] Question regarding box size

Victor Rosas Garcia rosas.victor at gmail.com
Fri Jul 10 18:35:05 CEST 2015

You can reduce the box size with editconf.  If you start with a protein,
you can add a layer of water of a given thickness by using genbox.

Hope this helps


2015-07-10 0:35 GMT-05:00 James Lord <jjamesgreen110 at gmail.com>:

> 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
> genconf
> -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
> now.
> https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing
> Cheers
> James
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