Solvate

a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations. Solvate generates irregularly-shaped solvent volumes, adapted to a given solute's structure; allows efficient computation of boundary forces as required in molecular dynamics simulations; guarantees a minimal solute-boundary-distance; allows to specify a minimum solvent surface curvature in order to avoid flat' surface regions; generatesdisordered' (= fluid) water, not a grid of water molecules (= ice); locally minimizes the positions of all water molecules; optionally places salt ions obeying a Debye-HÃ¼ckel distribution; optionally places (and marks) buried water molecules; and is X-PLOR/CHARMm-compatible, i.e., input and output is in pdb-/psf-format.

Developers

Helmut Grubmuller

For a list of references, go to: http://www.mpibpc.mpg.de/home/grubmueller/downloads/solvate/References/index.html