List of available solvents

.pdb or .gro files to be used with the function solvate_atom. Note that you could also use custom solvent boxes to solvate a simulation cell.

Contents

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

water

  1. 864_spc.gro|.pdb % equilibrated SPC water box
  2. 864_spce.gro|.pdb % equilibrated SPC/E water box
  3. 864_tip3p.gro|.pdb % equilibrated TIP3P water box
  4. 864_tip4p.gro|.pdb % equilibrated TIP4P water box
  5. 864_tip5p.gro|.pdb % equilibrated TIP5P water box
  6. 96spc_hex_ice_h.gro|.pdb % equilibrated SPC hex-ice water box
  7. 96tip4p_hex_ice_h.gro|.pdb % equilibrated TIP4P hex-ice water box
  8. 864_swm4_ndp.gro|.pdb * Polarizable water v1
  9. 864_swm4_ndp_vds.gro|.pdb * Polarizable water v2

organics

500xEtOH.gro|.pdb % equilibrated SPC water box

mineral

  1. 1xPyro_Lee_Guggenheim_1981_alfabeta90.pdb
  2. Pyrophyllite.pdb
  3. Hexagonal layered particles - Pyrophyllite / Montmorillonite - Talc / Laponite

Conversion functions

  1. spc2tip4p(filename) % This function converts a .gro or .pdb file with spc water to some tip4p water
  2. spc2tip5p(filename) % This function converts a .gro or .pdb file with spc water to some tip5p water
  3. spce2tip4p(filename) % This function converts a .gro or .pdb file with spc water to some tip4p water
  4. tip3p2tip4p(filename) % This function converts a .gro file with spc water to some tip4p water


Published with MATLAB® R2022a