Supported Applications

Solvate

Description

a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.
Usage
To list all executables provided by Solvate, run: $ sbgrid-list solvate
Usage Notes

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.
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install solvate Available operating systems: Linux 64, OS X INTEL
Primary Citation*

H. Heller, M. Schaefer, and K. Schulten. 1993. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase. J Phys Chem. 97(31): 8343-8360.
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