Forrest
Forrest
An issue was seen in finding the MCS of two compounds due to slight conformational changes. This PR adds the ability to set up a set of restraints between two...
- Adds Local MD - Resolves #792 - Other minor aesthetic changes Currently this is implemented without the Interaction group. The logic becomes more complex as you have to construct...
The ownership and lifecycle semantics of wrapped objects is currently confusing and its easy to shoot yourself in the foot. An example of valid vs invalid code using a context:...
Move the pre-processing of the integrator parameters to the C++. Should also attempt to clarify the names _Originally posted by @maxentile in https://github.com/proteneer/timemachine/pull/789#discussion_r942600565_
## Goal * Enable C++ warnings to enforce more explicit behavior ## Solution * Select warnings to enable * Likely should enforce warnings as errors * Avoid these warnings for...
Going through several tests that we had skipped due to time, noticed that some no longer pass. * slow_tests/test_mtm_condensed.py::test_condensed_phase_mtm ``` assert np.abs(np.average(vacuum_torsions, weights=vacuum_weights)) < 0.1 E AssertionError: assert 0.11419770372703592 <...
## Goal * Provide control over the precision of jax ~* Avoid flake8 linting issues regarding imports not at top of file (#596)~ ## Issues * Jax on the GPU...
## Intent Right now to perform MBAR we have to compute energies over the entire system when the only portion of the system that actually changes is the lambda. This...
Refer to comment by @maxentile https://github.com/proteneer/timemachine/pull/813#discussion_r964960123 Look at using `scipy.optimize.minimize` or some other method to reduce the parameterization of alignment.
* Disables water sampling for solvent, doesn't seem to make a difference * Some random clean up of the example scripts that were from trying to use them to test...