[gmx-users] Standard volume of the simulation box

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 26 09:45:51 CEST 2016

Hi Sana,

There's no such thing as a standard volume. The key decision you have to
take is what distance there should be between periodic images, for which
the consensus view is that you need at least 2.0 nm. I typically use 2.25,
corresponding roughly to 9 layers of water, so the protein can stretch
without significant risk of direct interactions. That means setting up the
unit cell with a distance to the wall of 1.125 nm.

Hope it helps,


On Mon, Apr 25, 2016 at 5:27 AM, Sana Saeed <bioinformatic.lady at yahoo.com>

> hi
> how can i find the standard volume of the simulation box, that includes
> ligand, protein and water.
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
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Tsjerk A. Wassenaar, Ph.D.

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