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I read the following in the To Do page: "Animation / vibrations: The best way may be to use OBMol conformation support, and simply rotate through the list of conformers. Essentially these just supply …
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**Issue**
- The accept/reject is fine for SHO but looks too low for QHO
- ∆H is far too high.
| Av. acceptance rate : `~87%` | Av. acceptance rate : `~58%` |
| :-: | :-: |
| Measured av. change in `e…
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(This issue documents offline results from last weeks discussions between @CFGrote and @ax3l. @CFGrote can you please edit to correct wrong and add missing information? :) )
## Beamline Elements
Curr…
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In estimators.moments_XXXY, the arrays X and Y are centered at different means (namely (1/w)_sx, (1/w)_sy) if remove_mean=True and symmetrize=False. Isn't that inconsistent? I think they should be cen…
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GROMACS is a molecular dynamics simulation package, and should probably be in homebrew-science along with a competing molecular dynamics simulation package, LAMMPS (already in homebrew-science).
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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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Hi guys,
I'm in version 1.0.26. I run: `model.viewStates(ligand="resname MOL and noh")`. And got the following error:
What am I missing?
```
/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/…
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Specifically:
- sundials (see closed issues #29678, #29851): ODE/DAE solver often used in chemistry simulations
- cantera (see closed issue #29852): combustion thermodynamics & kinetics engine
- groma…
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In lines 38,39,51,52 of updateCobraToolbox.m should be = instead of ==
This prevents updating CTB from matlab. Correcting the code makes it work but still can't update because it complains that there…
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Hi all,
I'm trying to understand how would I load only a subset of features from a NetCDF Amber simulation file.
From the documentation of the [load](http://www.emma-project.org/latest/api/generated…