TIP3P, TIP4P & TIP5P — Jorgensen Group, Yale

Builder

Your molecule, in water.

Structure

Enter a SMILES string. Explicit hydrogens are added automatically.

Examples

Water model

Box size

Equilibrate with BOSS first?

Equilibrating adds density, RDFs and H-bonds. Either way the files include minimization and equilibration scripts.

Molecule net charge

Neutral molecules use 1.14*CM1A-LBCC charges; ions switch to 1.14*CM1A automatically.

You get

Files for GROMACS, OpenMM, LAMMPS, AMBER & BOSS
Your molecule with OPLS-AA parameters
Water box & counter-ions
Minimize & equilibrate scripts
3D view of the box

All folders describe the same system; each was checked against GROMACS by single-point energies. With BOSS equilibration you also get the density, radial distribution functions and hydrogen bonds.

What the run actually does

1 — Parameters. BOSS assigns the OPLS-AA parameters and computes 1.14*CM1A-LBCC charges (1.14*CM1A for ions) for your molecule.

2 — Immersion. BOSS places the solute in its stored, pre-equilibrated water box and discards the waters that overlap it worst — one per solute heavy atom.

3 — Files. The system is written for GROMACS, then for OpenMM, LAMMPS, AMBER and BOSS with the same parameters.

Optional — Equilibration. Metropolis Monte Carlo at constant temperature and pressure (NPT, 25 °C, 1 atm): the box breathes, the waters repack around the solute.

Optional — Averaging. A second pass accumulates the observables — average volume (density), radial distribution functions, solute–water energy components, hydrogen bonds.

Nothing is stored. The job runs in a temporary directory, results are kept in memory for about two hours for you to download, then cleared.

Results

Your solvated box.

Water structure: O–O radial distribution. g_OO(r) is water’s fingerprint — the first peak near 2.8 Å is the hydrogen-bonded first shell seen by X-ray and neutron diffraction.

Solvation shell: solute–water RDFs. How water arranges itself around — a sharp peak near 2.8 Å against a polar atom is a hydrogen bond; a soft rise near 3.5 Å is hydrophobic packing.

The box

Final Monte Carlo configuration — solute in color, waters as thin lines. Drag to rotate, scroll to zoom.

Water models

TIP3P, TIP4P & TIP5P.

	TIP3P	TIP4P	TIP5P
q(H), e	+0.417	+0.520	+0.241
Negative charge	O: −0.834	M: −1.040, 0.15 Å from O	2 L: −0.241, 0.70 Å, 109.47°
σ(O), Å	3.15061	3.15365	3.12
ε(O), kcal/mol	0.1521	0.1550	0.16
Density, g/cm³ (25 °C)	1.002	1.001	0.999

All three: rigid, r(OH) 0.9572 Å, ∠HOH 104.52°. Experimental density 0.997 g/cm³. Densities from Jorgensen & Tirado-Rives, Proc. Natl. Acad. Sci. USA 2005, 102, 6665. TIP4P-Ew, TIP4P/2005 and CHARMM’s TIP3P are different models.

How to cite

References.

TIP3P and TIP4P: Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926–935. doi:10.1063/1.445869

TIP5P: Mahoney, M. W.; Jorgensen, W. L. J. Chem. Phys. 2000, 112, 8910–8922. doi:10.1063/1.481505

OPLS-AA: Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225–11236. doi:10.1021/ja9621760

1.14*CM1A-LBCC charges (neutral molecules): Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2017, 121, 3864–3870. doi:10.1021/acs.jpcb.7b00272

1.14*CM1A charges (ions): Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264–16270. doi:10.1021/jp0484579

BOSS: Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297