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-Hückel 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

Categories

Computational Chemistry

Versions

  • Solvate (os: Linux 32 vers: 1.0.1)
  • Solvate (os: Linux 64 vers: 1.0.1)
  • Solvate (os: OS X INTEL vers: 1.0.1)

References

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

License Type

This software is distributed under an Open license.


Static link to the SBGrid Solvate page.

Website Manual

Website Manual