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
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,
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.
- Download the water boxes here for TIP4P-Ew
- Unpack them with tar in a suitable directory
- To solvate with any of the TIP4P-Ew boxes use the following
- loadOff TIP4PEWBOX1
change 1 to any number between 1 and 40
- Instead of solvating with TIP4PEWBOX you should
solvate with SBOX, e.g.
solvateOct x SBOX 8
where x is the entity you want to solvate and 8 is the
radius as usual.
To solvate with TIP3P instead, just change TIP4PEWBOX to TIP3PBOX.
The water boxes exists locally in /away/bio/Data/Amber/
Samuel Genheden 5/10-10
- TIP4P-Ew in /away/bio/Data/Amber/Tip4pew_boxes/
- TIP3P in /away/bio/Data/Amber/Tip3p_boxes/