Polarizable Water

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Last Updated: Thursday, 22 August 2013 09:00

Polarizable water

In this part of the tutorial we will convert water in an existing Martini-system to polarizable water. In the polarizable Martini paper* the model is described as follows:

"The polarizable CG water consists of three particles instead of one in the standard Martini force eld. The central particle W is neutral and interacts with other particles in the system by means of the Lennard-Jones interactions, just like the standard water particle. The additional particles WP and WM are bound to the central particle and carry a positive and negative charge of +0.46 and -0.46, respectively. They interact with other particles via a Coulomb function only, and lack any LJ interactions. The bonds W-WP and W-WM are constrained to a distance of 0:14nm. The interactions between WP and WM particles inside the same CG water bead are excluded, thus these particles are "transparent" toward each other. As a result the charged particles can rotate around the W particle. A harmonic angle potential with equilibrium angle phi = 0 rad and force constant Kh = 4.2 kJ mol-1 rad-2 is furthermore added to control the rotation of WP and WM particles and thus to adjust the distribution of the dipole momentum."

If you want to solvate a new system with polarizable water, follow the steps in the protein part of the Martini tutorial, section 6. Instead of a normal waterbox and .mdp/.itp fi les use the waterbox containing polarizable water and polarizable Martini .mdp and .itp fi les (available from the Martini website: http://cgmartini.nl). Note that minimizing a polarizable Martini system requires some tweaking, as described below.

If you have an existing system with normal Martini water and want to change to polarizable water you may use the python script triple-w.py. For this example we convert dppc_bilayer.gro/dppc_bilayer.top available here.

1. Create a new gro file:

triple-w.py dppc_bilayer.gro

The python-script triple-w.py adds positive and negative sites at a small distance to every central water bead in a .gro file.

2. Adapt the .top file. Make sure the polarizable version of the particle defi nition martini_v2.P.itp fi le is included. In the .mdp file the value of epsilon_rc has to be adapted and the index group W renamed into PW (Download an example here). The .itp files for the lipids and possibly other molecules do not have to be changed.

3. If polarizable water is used in combination with proteins or peptides, all AC1 and AC2 beads have to be replaced by normal C1 and C2 beads. AC1 and AC2 are obsolete in polarizable Martini.

4. Minimize the system. For polarizable water to minimize without problems, it is SOMETIMES necessarry to change the constraints to stiff bonds. Using the ifdef-statement in the martini v2.P.itp fi le, this can be set using a de fine value in the .mdp fi le (have a look at the bottom of martini v2.P.itp to see how it works).

5. Set the correct options in martini_v2.P_example.mdp (e.g. "integrator = steep", "nsteps = 50", "constraints = none", "epsilon_r = 2.5", etc.) and the "defi ne" option to -DEM and change the W index group name.

6. Generate the input fi les for the minimization run:

grompp -f martini v2.P example.mdp -c dppc-polW.gro -p dppc bilayer.top -o em -maxwarn 1

7. Proceed with equilibration and production runs.

 

*S.O. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink, Polarizable Water Model for the Coarse-Grained MARTINI Force Field, PLoS Comput. Biol. 6, e1000810, 2010