Waterball interface
Boundary potential for MD simulations carried out in spherical water droplet. Two potentials are implemented and can be selected by keyword waterball_type:
- Harmonic: Harmonic potential (waterball_fconst) is applied to waters getting out of a sphere with defined radius waterball_radius (described in [1]).
- Potential of Beglov & Roux[2]: Uses adaptive sphere radius to maintain constant pressure of 1 atmosphere. It is the model recommended for use, as it gives better properties of water than simple harmonic potential. The implementation here is only partial, 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, and is pricipaly similar to the hard sphere model of Karplus[3]
Input file must be a PDB with water residues named WAT.
Keywords
References
[1] R. Sankararamakrishnan, K. Konvicka, E. L. Mehler, H. Weinstein, Solvation in simulated annealing and high-temperature molecular dynamics of proteins: a restrained water model, Int. Journal of Quantum Chemistry 7, 147-186, 2000
[2] 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
[3] A. Brunger, C. L. Brookds III, M. Karplus, Stochastic boundary condition for molecular dynamics simulations of ST2 water, Chemical Physics Letters 105(5), 495-498, 1984