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Hello,
Discussing with @amorgat about how Rhea and GO represent biochemical reactions, here are a few points to consider:
- in Rhea each reaction is represented by a 'master' (undefined directi…
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Extend the energy function you wrote in exercise 1d) (#5), so it can calculate the energy of polymer-systems. As mentioned in the introduction, covalent bonds bind monomers within the same polymer, th…
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Hi,
For talktorial 8 for accessing RCSB I think RCSB is having issue with not having all the ligands under the field `["rcsb_entry_info"]["nonpolymer_bound_components"]`. For instance I am using M…
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.carbon is an acceptable filename extension, but I could imagine something shorter like ex. .cb(CarBon) or .cn(CarboN) or .ca(CArbon) or .car(CARbon) to be more ergonomic. If a removal of the .carbon …
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https://github.com/TRI-AMDD/htp_md/blob/26db9da9233dbb2a1565f2bcc2e4ec21c990b204/src/htpmd/ml_models/polymernet/data.py#L60
@shenggong1996:
Two trajectories (0603/lit_0.7/WZ9/ and 0603/lit_0.7/W…
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Hei, I've used Opendrift previously to track particles on the Norwegian Continental Shelf (NCS), I need to run some simulations again. Earlier I was reading ocean currents data using
`SVIM = reade…
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**Describe the bug**
https://userguide.mdanalysis.org/stable/examples/analysis/polymers_and_membranes/hole.html does not render as html but looks like a notebook (similar to #175)
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Hi Andrew. I've been looking at scripts (sh) but I'm not very good with this programming language, I didn't understand it very well. I'm in doubt about the `bonds_type` property of the `GPSettings` cl…
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@soycapitan, for each realization there is the energy that corresponds to the chain formation just before docking (@NKruszewska you can explain). Please plot entropy of particular realization as the …
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Hello,
I'm trying to generate a polymer melt of dextran, and I saw that someone else had a similar problem with another polymer not having an angle or something, does something need to be updated h…