SIIT - solvent induced independent trajectories

This page contains instructions how to generate independent starting structures for MD simulations by employing different water boxes.

This method is described in S. Genheden, U. Ryde (2010) "A comparison of different initialisation protocols to obtain statistically independent molecular dynamics simulations" J. Comput. Chem. DOI: 10.1002/jcc.21546

The water boxes are in the leap-format off and so this guide is for the leap program of the Amber package.
We provide boxes for both the TIP4P-Ew and TIP3P water models.
The water boxes are named TIP4PEWBOXn or TIP3PBOXn, where n is 1, 2, ..., 40.
  1. Download the water boxes here for TIP4P-Ew or TIP3P
  2. Unpack them with tar in a suitable directory
        tar -xjf waterboxes.tar.bz2
  3. To solvate with any of the TIP4P-Ew boxes use the following leapcommands:

  4. To solvate with TIP3P instead, just change TIP4PEWBOX to TIP3PBOX.
You can put your water boxes in a directory where they are easily accessible to all of your projects, then you can just add a path when you start leap, e.g.
   addPath /temp2/Waterboxes/

Local information

The water boxes exists locally in /away/bio/Data/Amber/ Samuel Genheden 5/10-10