GOMC parser

Hi,

I implemented GOMC parser for alchemlyb and you can find my implementation in my GitHub.

I have few questions about alchemlyb and I would appreciate your help and suggestion.

1. In alchemical-analysis, if PV value was available, was added to u_nk. However, in alchemlyb, Total Energy is also added to u_nk. Is there any reason you chose different approach?

2. In MBAR documentation it is mentioned that The MBAR method is only applicable to uncorrelated samples from probability distributions. Is there any appropriate series that can be applied to Monte Carlo results for equilibrium_detection, statistical_inefficiency, and more ?

[mrshirts]

2- Using soft core distance for coulomb interaction, would not cause error in long range electrostatic energy (Ewald summation method)?

Usually one would use soft core for the short range coulomb, and linear coupling for the long range Ewald summation.

[msoroush]

Neglecting the intermolecular van der Waals is an approximation, and I really don’t know how big it is. But that is question that should be independent of the analysis.

Just to be clear, I am not neglecting the intra nonbonded energy in my simulation. I only couple the nonbonded energy with lambda. When I evaluate the Boltzmann weight (-Beta * change in energy acting on the same configuration space), bonded and intra nonbonded energy will cancel out, since the solute’s configuration is same.

This is a snapshot of Bennett paper:

If your energy differences that you stick into MBAR are not actually the differences between the energies that are used in the Boltzmann weighting of the configurations (which could happen by neglecting intramolecular interactions), the free energies coming out of MBAR won’t be correct.

I feed (deltaE + PV + totalEnergy) to MBAR, where deltaE is change in energy (nonbonded and long range correction), PV (if we are doing NPT simulation), and total energy (as discussed in issue #62)