Your molecule in TIP3P, TIP4P or TIP5P water, ready to run in GROMACS, OpenMM, LAMMPS, AMBER or BOSS.
Powered by BOSS — the group's Monte Carlo engine does the work behind this form.
Before you can simulate a molecule in water, a molecular-dynamics program needs the whole system: the molecule with its force field, thousands of water molecules around it, ions to balance its charge, and a box relaxed to the right density — each in the format that program expects. Building it by hand is slow and easy to get wrong.
TIP3P, TIP4P & TIP5P does it in one step. Give it a molecule — as a SMILES string, a drawing, a name or a structure file — and BOSS, the group’s simulation engine, gives it OPLS-AA parameters and CM1A partial charges, builds a box of TIP3P, TIP4P or TIP5P water around it, adds counter-ions and optional salt, and relaxes the whole box by Monte Carlo at your temperature. The same system is written for GROMACS, OpenMM, LAMMPS, AMBER and BOSS, with the scripts to minimize, equilibrate and run 100 ns.
TIP3P and TIP4P were developed in the group in 1983, and TIP5P in 2000; TIP3P is the most widely used water model in molecular simulation. Here they come with your molecule already in them, in a few minutes, with nothing to install.
| 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, 6665–6670. TIP4P-Ew, TIP4P/2005 and CHARMM’s TIP3P are different models.
| BOSS Quick Start | TIP3P, TIP4P & TIP5P this page | Organic Solvents | LigParGen | |
|---|---|---|---|---|
| It answers | What shape does my molecule take, and how does it behave in water? | How do I get my molecule into a box of water, ready to simulate? | How do I get my molecule into an organic solvent? | What numbers does my MD program need for this molecule? |
| You get | The most stable shape, hydration free energy, dipole, surface area | Your molecule in thousands of water molecules, with ions, relaxed by BOSS | Your molecule in 512 solvent molecules, relaxed by BOSS | Force-field parameters |
| Files for | Docking, quantum chemistry, viewing | GROMACS, OpenMM, LAMMPS, AMBER, BOSS — ready to run | BOSS, GROMACS, OpenMM, LAMMPS — ready to run | GROMACS, OpenMM, CHARMM and 7 more |
| Solvent | Continuum water (GB/SA) | Real water molecules | Seven organic solvents | None |
| Time | Seconds to a few minutes | A few minutes | A few minutes | A few seconds |
Find your molecule’s best shape with BOSS Quick Start → then put it in real water here, or in another solvent on Organic Solvents — or take only its force field from LigParGen.
Final Monte Carlo configuration — your molecule in color, waters as thin lines. Drag to rotate, scroll to zoom.
Runs now use BOSS 5.1. Most molecules go into BOSS's standard box of 512 waters, as in BOSS's test job for a molecule in water, instead of a box cut to a chosen layer; only molecules longer than about 15 Å still get a larger box. Every run now starts at constant volume, as BOSS's manual advises, before the box relaxes at 1 atm.
After an update on 7 October the service took about four minutes to come back, and runs started in that time failed. Updates now wait for the old service to stop before the new one starts.
TIP4P carries its negative charge on a massless point (M) next to the oxygen. It belongs in the simulation files, but the 3D view drew it as an extra atom on every water. The view now hides it.
The structure behind the 3D view was shifted by one column, so the viewer lost track of which atoms were hydrogens and drew the waters as a web of lines. The columns are fixed, and the daily check now verifies them.
Adding the tool's header to system.prmtop removed one of the file's sections (%FLAG POINTERS), so AMBER refused to read it. The header is now added without touching the rest of the file, and the daily check opens every prmtop to confirm the section is there.
If a run failed for you and your problem is listed here, please run it again.
calculations run since launch
Calculations that finished on this page since it went live, counted by country. Each run is recorded only with its date, country and whether it worked.
The README in your download lists exactly the papers that apply to it.
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
BOSS: Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689–1700. doi:10.1002/jcc.20297
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
CM1A charges (charged molecules, unscaled): Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264–16270. doi:10.1021/jp0484579