README.md

OPLS-aa parameters for perfluoroalkanes

• Source: Watkins and Jorgensen, J. Phys. Chem. A, 105, 2001 pp 4118-4125 http://dx.doi.org/10.1021/jp004071w

• Forcefield file initially created 04 August 2017 by C.R. Iacovella

Source Notes:

While all parameters are listed in Watkins and Jorgensen, bond and angle parameters have various original sources, as detailed in the manuscript.
These are summarized below:

• CT-F Bonds come from reference http://dx.doi.org/10.1002/jcc.540130806
• F-CT-F angles are from reference http://dx.doi.org/10.1021/ja00124a002
• CT-CT-F angles are the same as CT-CT-OH and CT-CT-OS from reference: http://dx.doi.org/10.1021/ja00124a002
• Bonds and angles for the CT-CT and CT-CT-CT are the same as for alkanes from reference, http://dx.doi.org/10.1021/ja9621760

Additional Notes:

• These are the "general" parameters for perfluoroalkanes; specific dihedrals exist for 4 and 5-mers
• The backbone dihedral specifically references opls_962 (i.e. C-CF2-C) rather than only using the "CT" class; if only the "CT" class were used, this would create a conflict with alkane systems if the parameters were merged.
• To be consistent with conversions performed by OpenMM (http://openmm.org)
  • The original parameters are defined as kcal/mol, this file uses kJ/mol; a conversion factor of 4.184 was used.
  • PI is defined as 3.141592653589 for conversion to radians.
• Atom type names, e.g., opls_961, correspond to those defined in the OPLS forcefield itp file distributed with GROMACS.
• Conversion from OPLS-style dihedrals to RB follow the formulas detailed in the GROMACS manual (http://gromacs.org).
  • Specifically, the OPLS form is given as:

0.5*(F1*(1+cos(phi))+ F2*(1-cos(2phi))+ F3*(1+cos(3phi))+F4*(1-cos(4phi)))

• The RB mapping:

c0 = F2+0.5*(F1+F3)
c1 = 0.5*(-F1+3F3)
c2 = -F2 + 4F4
c3 = -2F3
c4 = -4F4
c5 = 0

• Example molecules with correct atomtypes are defined as test cases. Execute the testing script using py.test -v --tb=line

Force field DOI