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Analyze compute the energy difference between the wrong states

See original GitHub issue

The function analyze.analyze() extracts from the ncfile the number of states without taking into account the presence of the fully interacting state, and ends up computing the free energy difference between the fully interacting state and the next to last state for each phase here

# Accumulate free energy differences
entry = dict()
entry['DeltaF'] = Deltaf_ij[0,nstates-1]
entry['dDeltaF'] = dDeltaf_ij[0,nstates-1]
entry['DeltaH'] = DeltaH_i[0,nstates-1]
entry['dDeltaH'] = dDeltaH_i[0,nstates-1]
entry['DeltaF_restraints'] = DeltaF_restraints
data[phase] = entry

In general, since we treat the fully interacting state as special, we need to be careful during the analysis.

I’ll soon open a PR with the fix.

Issue Analytics

State:
Created 7 years ago
Comments:5 (5 by maintainers)

Top GitHub Comments

1reaction

Lnadencommented, Oct 14, 2016

Ah, yes, good catch. It may be better to just replace [0,nstates-1] with [0,-1] to make it independent of how much shifting we do at the head of the row.

0reactions

andrrizzicommented, Oct 18, 2016

Closing this to open a better titled issue.

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