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I'd like to implement something along the lines of CAMS (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113119) to provide live visualisation of local stress in a molecule during i…
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A function that takes a parameter/parameter path and lists all formulas resp. parameters/reactions etc. where this parameter is used in a simulation.
@Yuri05 @msevestre Do you think it can/should b…
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At present, the unit tests mostly cover the `charmm_containers` module. This is intentional - these classes have been the source of most of the issues I've discovered in the past - but issues with `Mo…
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@jchodera brings up that we should make sure chemical state key can accommodate changing both a small molecule and a protein sequence in the same simulation. Perhaps a `dict`, as suggested by John, wo…
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It might be useful to switch between stochastic and deterministic simulation based on the time step and molecule counts of each reaction. For example, stochastic complexation is currently finding the …
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I've got an input SMILES string for which bingo produces different similarity results depending on whether the indexed molecule is provided as inchi or SMILES. I need to have the similarity results b…
twall updated
2 years ago
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Is it possible to implement the simulation of particles with partial charges, e.g. coarse graind molecules with partial charges?
I think we only need to add these features:
1. add particle attribute…
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Develop a minimal viable product (MVP) for integration of SpringSalad into VCell.
### Motivation
VCell supports agent-based rule based simulations using NFSim, and non-rule-based particle simulati…
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It's easy enough for the client to not render water molecules at will, but for large simulations the inclusion of water in frame data is wasteful and more critically might blow over the size limits of…
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**Summary !!!**
- **BioModel Name**: Menichetti2019 - Drug−Membrane Permeability across Chemical Space
- **BioModel Tag**: Machine learning model, Ersilia
- **Metadata Comments**:
What type…