Solvate example

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Helmut Grubmüller
Director
Phone:+49 551 201-2300Fax:+49 551 201-2302

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Department of Theoretical and Computational Biophysics

Solvate

Helmut Grubmüller and Volker Groll

Support: DFG (SFB 143/C1 and 533/C1)


SOLVATE is 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,
  • generates »disordered« (=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.

SOLVATE was written by Helmut Grubmüller and Volker Groll in the Theoretical Biophysics Group of Paul Tavan at the Institute for Medical Optics, University of Munich.

 
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