OpenMM forcefields

Since OMMProtocol is compatible with a multiple formats thanks to OpenMM itself and other excellent packages (MDTraj, ParmEd…), you can use the forcefield formats defined in other MD suites. Namely, PRMTOP for Amber, PSF+PAR+STR in CHARMM or TOP in Gromacs. If you are already using some of those packages, you don’t need to do anything else: just provide the paths in the topology section (CHARMM parameters must be specified in charmm_parameters).

However, OpenMM does provide its own set of forcefields, converted from the original formats (Amber, Charmm and others) to its FFXML format. The following section lists all the built in forcefields in OpenMM as of v7.2. The updated list will be available at the OpenMM repo.

amber14/DNA.OL15.xml
amber14/DNA.bsc1.xml
amber14/RNA.OL3.xml
amber14/lipid17.xml
amber14/protein.ff14SB.xml
amber14/protein.ff15ipq.xml
amber14/spce.xml
amber14/tip3p.xml
amber14/tip3pfb.xml
amber14/tip4pew.xml
amber14/tip4pfb.xml
charmm36/spce.xml
charmm36/tip3p-pme-b.xml
charmm36/tip3p-pme-f.xml
charmm36/tip4p2005.xml
charmm36/tip4pew.xml
charmm36/tip5p.xml
charmm36/tip5pew.xml
charmm36/water.xml
absinth.xml
amber03.xml
amber03_obc.xml
amber10.xml
amber10_obc.xml
amber14-all
amber96.xml
amber96_obc.xml
amber99Test.xml
amber99_obc.xml
amber99sb.xml
amber99sbildn.xml
amber99sbnmr.xml
amberfb15.xml
amoeba2009.xml
amoeba2009_gk.xml
amoeba2013.xml
amoeba2013_gk.xml
charmm36.xml
charmm_polar_2013.xml
hydrogens.xml
iamoeba.xml
pdbNames.xml
residues.xml
spce.xml
swm4ndp.xml
tip3p.xml
tip3pfb.xml
tip4pew.xml
tip4pfb.xml
tip5p.xml

To use them with a PDB file, just specify them in a list for the forcefield key, like:

topology: some.pdb
forcefield: [amber99sbildn.xml, tip3p.xml]

or, if you prefer this other syntax:

topology: some.pdb
forcefield:
- amber99sbildn.xml
- tip3p.xml

More forcefields

The OpenMM team is doing a tremendous effort towards the next release, which will include even more forcefields. You can check the progress here. This will include more builtin forcefields and also a separate package called openmm-forcefields, developed here. When this is available, it will be shipped with OMMProtocol.

Custom forcefields

While the best option to generate custom parameters is to use something like AmberTools to create a PRMTOP topology and use that, there are options to develop custom parameters with OpenMM. Check these links for further information:

  • Creating and Customizing Force Fields in OpenMM (YouTube video).
  • openmm-forcefields also features Python converters for Amber & CHARMM forcefields. As a result, automated tooling for those forcefields can be used and then converted to OpenMM, like antechamber or cgenff.
  • openmoltools (included with OMMProtocol) provides some functions to process and convert forcefields. Specifically, openmoltools.amber.run_antechamber for parameterizing small molecules through AmberTools’ antechamber, and openmoltools.utils.create_ffxml_file to convert the result to OpenMM XML forcefield format.