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Dear sirs, thank you for this program to visualize organic molecules for classes. But: It is possible to build "impossible" molecules! Like: a 5 membered ring of Nitrogens with triple bonds between ea…
cryos updated
8 years ago
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# Solvation models
Electrostatic and solvation models can be roughly divided into two classes (Warshel, 2006; Roux 1999; Ren, 2012) explicit solvent models that treat the solvent in atomic detail and…
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python.c is messy. Moving some of the input gathering and setting up of the structure would help. There's an example implementation here: https://github.com/jhmatthews/python/commit/6c653b6d5948f5efde…
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@VijayPande has recently brought up the issue of creating a top level "OpenMM application" for running simulations without writing any code. We've discussed this idea a few times before, but could ne…
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If you use the new optking feature that allows freezing of individual Cartesian coordinates _without_ also setting `no_reorient` and `no_com`, the molecule reportedly turns into a "high-speed car wrec…
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The Z-matrix builder for gaussian starts only at line 3! In 0.8.1, the matrix is generated correctly.
Example:
C
C
O r2
...
Reported by: *anonymous
cryos updated
8 years ago
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The Z-matrix builder for gaussian starts only at line 3! In 0.8.1, the matrix is generated correctly.
Example:
C
C
O r2
...
Reported by: *anonymous
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Could you change input dialog to make possible load outputs of computational programs with non-OpenBabel extensions. For example, *.out extension is widely used, and default extension for GAMESS US is…
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It appears that when the load_pdb_rcsb() executes it does not grab the bfactor data from the pdb file. When I run the following python code the bf array is zero when in fact it should have values (see…
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I'm not sure where the best place to discuss Optim is so I'll post this here.
In my field, computational chemistry, it is common to enforce a maximum step size constraint at each optimization step, w…