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deGrootLab / pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
GNU Lesser General Public License v3.0
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How to interpret wplots? #42

Open DreamCykl opened 9 months ago

DreamCykl commented 9 months ago

Hi,

I've been using the pmx module for a while now to create single-topology merged molecules. While I have a good understanding of most of the output, I havevn't found documentation explaining how the wplots should be interpreted.

I have two plots here, showing a transition from ligand A -> ligand B, in complex with protein. image image

Am I right in thinking that the overlap of the two histograms indicates good convergence? And more overlap reflects more overlap of the forward and reverse snapshots? With EQ FEP I believe you expect the forward and reverse energy values to converge towards the end of the time-series. Is this the same with non-EQ FEP? Or would good convergence / overlap of the forward/reverse work values be more present over the whole graph?

Thanks.

vgapsys commented 8 months ago
  1. Convergence looks fine. pmx analysis also gives a quantitative estimate for convergence
  2. Larger overlap of the work histograms corresponds to better convergence
  3. Two converged equilibrium FEP simulations at neighboring lambda windows should give similar work distributions to those that you have here
  4. I don't know what you mean with "present over the whole graph"