Error in computePMF example

[trendelkampschroer]

I think I've spotted an error in the examples section of the MBAR.computePMF funcion. But it could also be me geting confused with the indices

>>> from pymbar import oldtestsystems
>>> [x_kn, u_kln, N_k] = oldtestsystems.HarmonicOscillatorsSample(N_k=[100,100,100])
>>> mbar = MBAR(u_kln, N_k)
>>> u_kn = u_kln[0,:,:]

If $u_{kln}=u_l(x_n^{(k)})$ shouldn't it be

>>> u_kn=u_kln[:, 0, :]

in the 3rd line?

In other words don't you use the potential energy at fixed state $l_0$ for data generated at different thermodynamic states $k$ to estimate the pmf at the desired state $l_0$?

[jchodera]

Yes, that's an error, all right!

[jchodera]

@kyleabeauchamp: Can you fix this?

[kyleabeauchamp]

Done