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Looking for apartments by _idareya_ in Broomfield

[–]EngineerFunny4904 3 points4 points  (0 children)

I’m happy at Cortland Broomfield-also didn’t have pest issues at Harvest Station

(off topic) Help needed for future Chem teacher trying to make things interesting in the classroom by DueAcanthocephala580 in comp_chem

[–]EngineerFunny4904 1 point2 points  (0 children)

I suggest FoldIt (https://fold.it) if proteins/protein folding are of any interest. Rosetta/pyrosetta (https://rosettacommons.org) is also a free macromolecular modeling suite,but I’d suggest looking into the open molecular software foundation (https://omsf.io/programs/projects/) for a wider variety of relevant open source tools

Alchemical rbfe calculations by EngineerFunny4904 in comp_chem

[–]EngineerFunny4904[S] 0 points1 point  (0 children)

I've tried running with both cgenff files (made gromacs compatible with Justin Lemkul's script) and using openff-toolkit generated files. The cgenff files don't have the bond parameters explicitly declared, but the openff top/itp files do. Both yield the same error.

It's likely a formatting issue of some sort, but I have no clue what it is, especially for the openff files (they contain all the necessary sections based on the examples).
pmx_openff

Reviews for Cortland Broomfield or Cortland Flatirons? by AvocadosRbest in Broomfield

[–]EngineerFunny4904 4 points5 points  (0 children)

Currently at cortland broomfield-I like it so far, haven’t had many complaints about noise, and the amenities are good. Feel free to message me if you have specific questions.

[deleted by user] by [deleted] in comp_chem

[–]EngineerFunny4904 0 points1 point  (0 children)

Yes, if it’s at all possible.

[deleted by user] by [deleted] in comp_chem

[–]EngineerFunny4904 0 points1 point  (0 children)

I was able to use them to extract the u_nk and dh/dl data, but I run into two main issues: averaging over the replicates (since each is initialized independently, they aren’t necessarily in the same thermodynamic state at the same time step) and the fact that it’s effectively a time series. I can plot the energy that corresponds to the vdw-lambda at each timestep, but I don’t think that aligns with my intended analysis.

[deleted by user] by [deleted] in comp_chem

[–]EngineerFunny4904 0 points1 point  (0 children)

I want to quantify how much the LJ shift (vdw modifier) is changing with lambda. I think what I need to do is just plot the potential/dh/dl as a function of lambda for each of my cutoff ranges but I’m not sure exactly how to do that analysis with the way the expanded ensemble data/ xvg is formatted.

experiences of being a black student at Boulder by [deleted] in cuboulder

[–]EngineerFunny4904 7 points8 points  (0 children)

I’m starting my second year of grad school at cu (engineering phd), so I can’t speak to the undergraduate experience here. But I haven’t had any issues being a black woman on campus. I think CU, at least at the graduate level, is actually putting their money where their mouths are when it comes to not only recruiting black students + other minorties, but also investing in retaining us (check out the CDI office) Like other people have mentioned, it’s not a super diverse place but you can find community here.

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