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I need to rapidly minimize conformations of organic molecules that are anywhere from 250-500 atoms in size (lignin polymers). I was using MMFF in RDKit before, but I would like to access the GPU accel…
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Currently, we have an issue where some converted AMBER protein force field files contain the prefixe `protein-` while others do not, causing seemingly straightforward operations like bringing in the p…
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While writing the code as per the [User's Guide](https://isicle.readthedocs.io/en/latest/user_guide/NMR.html) for NMR Chemical Shift Calculation in CREST Conformational Ensembles , there is a runtime…
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To help ensure that people are providing all the information required with a forcefield (e.g., Original source, who created it, etc.) it might be worth it to create what is basically just an XML vers…
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I wish to utilize the amber99sb-disp force field in OpenMM, which is proficient in describing Intrinsically Disordered Proteins (IDPs). I intend to combine it with OpenMM's metadynamics to accelerate …
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**Describe the feature**
Anyone planning to write workflows to retrain CHGnet with DFT for specific problems?
@janosh @matthewkuner ?
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Right now planckton-flow does not allow custom forcefields to be made. It would be nice to change this for new molecules we create in mbuild.
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Making perturb executable..
g++ -g -Wall -o ../perturb ./utils.o ./stringutils.o ./vector3.o ./matrix3.o ./matrix.o ./random.o ./config.o ./atom.o ./residue.o ./chain.o ./system.o ./pairint.o ./lji…
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Using the provided example output files from this package, I attempted to run a steepest descent minimization using typical parameters to test my installation. I get the following fatal warning at the…
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...only in Molecule._configure and anything requiring the energy/forces being known.
Consider making ff a kwarg that defaults to None, and raise errors if a ff is not specified in the above scenarios…