Free energy results
A "free energy results" data set contains all the information used to calculate the free energy of binding. Unlike the potential energy results, the goal should be a free energy that is independent of _all_ possible nonphysical parameters (vdW/Ewald cutoffs, barostat or thermostat method or time constant, multistep integrators, etc. So these nonphysical terms should be corrected for (or at least specifically mentioned that they are NOT corrected for).
Such a data set would include:
- All the inputs for the potential energy result (including the energies). This could be done by specifically linking to a "potential energy result", but perhaps would be better just including a separate set of run files.
- Program name and version used for both simulation
- Dynamical information such as timestep, barostat thermostat information. Again, this can best be provided by submitting the actual run files.
- NPT and NVT or NVT implicit solvent specified
- Method of analysis used to calculate free energy from simulation (TI, FEP, BAR/MBAR, WHAM) described, including program name and version if applicable.
- Length and number of simulations run
- Pathway used from initial to final state (alchemical (mathematical pathway described), PMF (in what variable), etc.)
- Final state used to connect free energies between solute and complex state (double decouple/annhiliation, testrainted end states)
- Any analytical correction used to correct the free energies.
- How statistical error bars are estimated.
Including this information would allow testing sampling methods and formalism, post-analysis methods, cutoffs, timesteps. Initially, these files will not be placed under explicit version control, though the wiki provides some level of version control. Eventually, for example, for potential energy results, we would like to keep versions for multiple versions of code.