Interface water_restraint

Modifier for QM/MM MD simulations, prevents mixing of QM waters around the defined solute with MM bulk waters. At the beginning of the simulations, specified number of water molecules cosest to the solute is tagged as QM waters. If this QM water moves farther than the closest bulk water, a harmonic restraint is applied to pull the QM water back towards the solute.

Methods and capabilities

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

Keywords used

Keywords specific for this interface:


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

# Water restraint example 1: Amber MD with water restraint

# Simple demonstration of the water restraint modifier. It is intended for
# QM/MM calculations but here it is used for simple MM dynamics to make the
# example run faster.

job: dynamics
init_temp: 300

# Ace-ala-nme dipeptide solvated with 18 water molecules
geometry: ace_ala_nme_waterball_18.pdb

# Use Amber interface with default forcefield
# (The interface must be configured properly)
interface: amber

# Add the water restraint modifier
modifiers: water_restraint

# Setup for the modifier
  qmmm_wat_center: ":2" # Selection defining the center of the QM region, here it is residue 2
  qmmm_wat_num: 8 # Number of QM waters
  qmmm_wat_k: 10.0 # Force constant of the restraining potential (kcal/mol/A)