cg_openmm

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Negative weights for conformational state expectation in free energy calculation

5

When taking the expectation of whether a structure is folded (1) or unfolded (0) on an mbar object, often the weights for folded state at high temperature are very small...

cwalker7

How to do enthalpy/entropy of configurational states

1

OK there are two difference scenarios: - Calculating the entropy and enthalpy as a function of T (or as a function of parameters). This is straightforward, as there is already...

mrshirts

Speeding up process_replica_exchange

2

I've noticed that process_replica_exchange in rep_exch.py can be pretty slow - particularly this block of code which writes the .dat file: ``` f = open(os.path.join(output_directory, "replica_energies.dat"), "w") for step in...

cwalker7

We should make sure the uncertainty calculated from the pymbar covariance matrix is right. This will also become relevant for the entropy and enthalpy of folding calculations.

cwalker7

I think we should do some reorganizing of the utility functions throughout cg_openmm. For example, the plotters are scattered in numerous places. The names of the modules could also be...

cwalker7

There are a bunch of functions in ens_build which look at the energies of non-native and native poses, classified based on a native contact fraction cutoff. Is this something we...

cwalker7

precision of positions stored in .nc file vs. pdb files

2

While updating the expectation native contacts code, I realized that loading in the positions to mdtraj through pdb files will reduce the precision quite a lot (4 decimal place vs....

cwalker7

Units issue in the distance() function in random_builder.py

1

For some reason, the units coming out of the distance() function (in random_builder.py) are nm^2 when used in the new native contacts code #61 , but nm when used in...

cwalker7

It would be useful to be able to skip an equilibration period (and maybe automatically determine that period from timeseries analysis), or set a stride parameter for analyzing very large...

cwalker7

The ensemble check physical validation tests on Travis are failing with a segmentation fault, when we do multiple of them (temperature pair option set to 'adjacent' or 'all'). For some...

cwalker7