Add comparison of water models #18
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mattwthompson
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This is what I get when I run it (takes maybe a half hour on rahman): https://gist.github.com/47105b78d41030ab0d96f4d509bfec81 |
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@ptc2ug may like seeing this 🙂 |
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I could use some eyes on the XMLs, they seem to accurately reproduce the reference I used (http://www1.lsbu.ac.uk/water/water_models.html#back1) but the RDFs are somewhat objectionable. |
rmatsum836
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rmatsum836
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I'm late to reviewing this. I made a few minor changes to the notebook but this LGTM. If anyone from @mosdef-hub/mosdef-contributors could add a review for this workflow, that would be great!
rsdefever
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rsdefever
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Overall the tutorial worked well. My only suggestion is to improve the instructions on installing the required packages. I tried everything in a fresh conda env and ran into a couple of snafus (see comments). These aren't a big deal but might be a barrier to entry for a new user of MoSDeF.
| numpy | ||
| mbuild | ||
| foyer | ||
| mdtraj | ||
| matplotlib |
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What about gromacs?
Also, there is no requirements.txt under the water-models tutorial.
And both water-box and water-models examples require openbabel to run.
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I added installation instructions in water-models.ipynb and added requirements.txt to that example as well. Gromacs can be installed from the bioconda channel and open babel can be installed from the open babel channel.
| "ax.plot(ref[:, 0], ref[:, 1], 'k-', label='Reference')\n", | ||
| "\n", | ||
| "ax.set_xlabel(('Simulation time, ps'))\n", | ||
| "ax.set_ylabel(('System density, kg/m^3'))\n", |
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The density seems to have periodic oscillations. Is this from Parrinello-Rahman + unequilibrated starting configuration? It may not matter for the purposes of this demo, just an observation.
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Thanks @rmatsum836. One other thing. The SPC/E link in the water-models example is dead. |
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#13