cg_openmm
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shirtsgroup
Tools to build coarse grained models and perform simulations with OpenMM
## Description Updates mbar functionality to work with pymbar version 4.0. A number of changes were made according to this guide: [https://pymbar.readthedocs.io/en/master/moving_from_pymbar3.html](https://pymbar.readthedocs.io/en/master/moving_from_pymbar3.html) MBAR solvers are now more reliable than version...
## Description Adds lots of new functionality for optimizing 1sc, 2sc, and 3sc helices: - **1sc helices** nonbonded optimization: we can now set any combination of bb-sc and bb-bb bonds,...
Figure out why this monomer definition fails to build with the random builder: ``` monomer_dict = { "monomer_name": A, "particle_sequence": [b,sa,sb,sc], "bond_list": [[0,1],[1,3],[0,2]], "start": 0, "end": 0, } ``` And...
Major changes to the pymbar API in version 4.0.1 need to be reflected throughout cg_openmm. See here: https://pymbar.readthedocs.io/en/master/moving_from_pymbar3.html
If we ever need this combination of Mie potential with binary interaction parameter custom mixing rules, can revisit the framework I started here: https://github.com/shirtsgroup/cg_openmm/commit/e6f603ebdf18f42839ef3089f8b7c26a31fc21e0#diff-e8dfc92764bdbb7fa37ed231cdaa988bc9fb319fffb733b34bc3985b03e3020aR705 Since the binary interaction (kappa) parameters...
When bootstrapping the individual state heat capacities with `bootstrap_partial_heat_capacities()`, KeyErrors can result when certain configurational states have low populations, leading to no data points in some bootstrap trials. One solution...
## Description Some assorted fixes and updates: 1. Applies the conformational state decomposition for native contact expectations. This is done in a similar way as the 'partial' heat capacity contributions...
For a 2 state model and a 3 state model, add an example where we compute and plot the partial heat capacities, population fractions, and state transition terms.
In the partial heat capacity function (the standalone non-bootstrapping version https://github.com/shirtsgroup/cg_openmm/blob/master/cg_openmm/thermo/calc.py#L407), the uncertainties in the partial heat capacities still need to be implemented. For now, we just get all the...
Right now, we can scan the forward and reverse orientations of a linear homopolymer chain which has end-to-end symmetry by setting `homopolymer_sym=True` in the fraction_native_contacts function, and the higher of...
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Tools to build coarse grained models and perform simulations with OpenMM