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Solvator
The Solvator helps you to create a realistic aqueous solvent environment around your biomolecule. You can
  1. solvate your molecule or
  2. generate a water box only for other purposes.
The Solvator also guides you to determine the dimension of your system with orthorhombic, hexagonal, octagonal, cylindrical, or spherical shapes of water box. It should be noted that the solvated system neither minimized nor equilibrated. One may obtain a slightly minimized solvated system in STEP3 of Quick MD Simulator.

Ions can be added in the simulation box by specifying ions (NaCl, KCl, and CaCl2) and concentration (C). The numbers of ions are automatically determined by the ion-accessible volume (V), the total charge of the system (Qsys), and the valence of the positive ion (z+),
  • N+ = CV - Qsys / (2e z+)
  • N- = z+CV + Qsys / 2e
to neutralize the total system charge, i.e., z+N+ - N- = -Qsys. The ion-accessible volume, V, is estimated by subtracting molecular volume from the total system volume. The initial configuration of ions is then determined through short Monte Carlo (MC) simulations (2000 steps) using a primitive model, i.e., scaled Coulombic and van der Waals interactions. By simply changing a variable of nmc in the input (step2.2_ions.inp), you can perform longer MC simulations on your local machine.
  1. Solvate your molecule..
    Download PDB File: Download Source:

    Upload PDB File:
    PDB Format: RCSB CHARMM

    Next Step:
    Select Model/Chain
    2. or..

  2. Generate a water box only..
    Select Water Box Type:
Next Step:
Generate Waterbox