Python Package for Generating LAMMPS Input Scripts for Alchemical Processes: generate_alchemical_lammps_inputs

The parsers featured in this module are constructed to parse LAMMPS output files, (i.e., dump files), containing data for given potential energy values (an approximation of the Hamiltonian), U_{𝞴,𝞴'}, at specified values of 𝞴 and 𝞴', where varies from one to zero scaling the potential between solute and solvent in a reversible manner. The system is equilibrated at a 𝞴-state and energy values are evaluated at alternative 𝞴 values denotes by, 𝞴'. Because generating the input files can be cumbersome, functions have been included to generate the appropriate sections. This includes input scripts that generate formatted output files for the case where U has a separable dependence on 𝞴 or for analysis using thermodynamic integration (TI), Bennett Acceptance Ratio (BAR), and Multi-state Bennett Acceptance Ratio (MBAR). These resulting output files are generally formatted text files which can be readily analyzed using the python package, alchemlyb*. An example is available for benzene solvated in water and a solvated Lennard-Jones dimer [DOI: 10.18434/mds2-3637].

*Certain commercial equipment, instruments, or materials are identified in this paper to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.