cg_openmm
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Tools to build coarse grained models and perform simulations with OpenMM
We should decide which linters to apply to cg_openmm, and integrate into the CI. Running flake8 on the current project results in some 18,000+ errors, mostly line too long, unused...
We want to be able to use mixing rules other than the standard Lorentz-Bethelot, to investigate things like weakening the sidechain-backbone interaction strength while keeping the other interaction strengths constant....
We have been setting include_torsion_forces to false when building to get around this, and then including them for the simulations. Figure out why it doesn't work in the random builder.
There are two ways of making lists with simtk units, which can cause issues when getting their values if we don't use some standard convention throughout cg_openmm. 1. a list...
We should be able to read the thermodynamic states at the end of an .nc file, and restart the simulation. Useful in the case that we didn't run a simulation...
We get this warning numerous times throughout the replica exchange simulations and analysis: `Warning: The openmmtools.multistate API is experimental and may change in future releases` There are also these pymbar...
Need to update documentation - some text still mentions Yank. The standardization of the docstrings and variable names throughout cg_openmm has gotten a bit off.
It seems that the energy spiking issue #86 may be due to an issue with the angle/torsion nonbonded exclusions. It seems that some nonbonded interactions are not being enforced. For...
When using a 10 or 20fs timestep, in the course of a simulation there will be energy spikes, up to the order of 1E12 kJ/mol. This is more prevalent for...
In parameters_free_energy.py, we have the loop: for i in range(len(full_T_list)): U_n = unsampled_state_energies[i,:] # compute expectations of being in conformational state n # Store results in a dictionary results[str(i)] =...
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Tools to build coarse grained models and perform simulations with OpenMM