Interface water_ball

Spherical boundary potential for MD simulations in water. The interface implements only the mechanical component of the potential of Beglov & Roux[1] which uses adaptive sphere radius to maintain a constant pressure of 1 atmosphere. The electrostatic interaction of the solvent with the cavity is not calculated, nor is the angular correction described in the paper. Even this partial implementation yields results sufficient for use. The electrostatics can be covered by using a suitable implicit solvent model in the underlying calculation

1. D. Beglov, B. Roux, Finite representation of an infinite bulk system: solvent boundary potential for computer simulations, Journal of Chemical Physics 100 (12), 9050-9063, 1994

Methods and capabilities

The interface implements a single unnamed method; 'method' keyword not necessary

Keywords used

Keywords specific for this interface:

• waterball_center
• waterball_solute
• waterball_solute_k

Examples

The following examples, along with all other files needed to run them, can be found in the directory cuby4/interfaces/water_ball/examples

#===============================================================================
# Waterball modifier example
#===============================================================================

# 1000 steps of molecular dynamics using the default AMBER forcefield
# This input assumes that AMBER interface is already configured

job: dynamics
init_temp: 300
maxcycles: 1000
interface: amber

# Geometry: ace-ala-nme solvated with 124 water molecules
geometry: ace_ala_nme_waterball.pdb

# Apply the water_ball modifier
modifiers: water_ball

# Setup for the modifier
modifier_water_ball:
  # The droplet is centered on the solute
  waterball_center: solute
  # The solute is defined as the first three residues in the PDB file
  waterball_solute: :1-3