jmelcr / martini_openmm Goto Github PK

An implementation of the Martini CG force field in OpenMM.

This is alpha quality software. Use at your own risk. Testing on your specific system is recommend. See the tests directory for example scripts to compare gromacs and openmm energies and forces.

Please report any defects as issues on the github repo.

The system has been tested on the sytems in the tests directory and works for:

• Martini v2
• Simple and complex mixtures of lipids
• Simple simulations of soluble proteins

It has not yet been tested for:

• Elastic network models of proteins
• ElNeDyn models of proteins

There has not yet been any effort to support:

• Martini v3
• Polarizable Martini

Limitations:

• Math in .itp files:
  • Gromacs allows for mathmatical expressions to be used in .itp files
    • 1 6 1 0.98112 RUBBER_FC*1.000000
  • This is not allowed in OpenMM and must be edited
    • 1 6 1 0.98112 RUBBER_FC
• The only supported electrostatic option is coulombtype = reaction-field
• The only supported option for Van der Waals is vdw_type = cutoff
• The cutoff must be the same for rcoulomb and rvdw