Add liquid box creation and simulation files #149
Conversation
|
I also wrote somethings similar using the python packmol handles John developed in |
|
@hjuinj - yeah, I added those (or at least some of them) for use in solvationtoolkit (github.com/mobleylab/solvationtoolkit). I haven't extended that for SMIRNOFF yet but I should. |
Added some formatting to the markdown in the readme file.
| - OpenEye tools (for creating molecule from SMILES and conformer generation) | ||
| - openmoltools (OpenEye conformer generation wrapper) | ||
| - Gromacs 4.6.7 (for calling genbox to create solvent box) | ||
| - ForceBalance 1.5.x (for putting information back that was thrown away by genbox) |
There was a problem hiding this comment.
Not ideal to have ForceBalance and GROMACS dependencies, but probably OK for the time being.
| float | ||
| Length of a cubic solvent box in nm. | ||
| """ | ||
| # Calculate total mass of the box in kg |
There was a problem hiding this comment.
Actually what about just using the approximate_volume_by_density function in openmoltools instead? openmoltools is already required here. Reduces code redundancy.
There was a problem hiding this comment.
I'm not necessarily opposed to merging this, but for the record I think it could be made a lot simpler by using SolvationToolkit to build the boxes (which can handle arbitrary solvents) and then the rest of the code could be considerably more concise I think, e.g. see the end of this Jupyter notebook I'd put together for a workshop in Chile: https://github.com/QCMM/workshop2017/blob/29b9f58046e4e85daee816995fb5b6944a333106/Free_energy_day1/OpenMM/Session2.ipynb
Still, maybe this is worth including as an example for now.
@leeping how about if we included this as an example for now and I put some notes in the README.md about how it could be simplified and/or dependencies reduced? Would that work for you?
|
It's fine to merge for now, I bet, but this will take more work to update for the topology branch as well. |
1 similar comment
|
It's fine to merge for now, I bet, but this will take more work to update for the topology branch as well. |
There was a problem hiding this comment.
@leeping did you see my comments? We can merge this now if you want, just wanted to make sure you saw them.
|
Will merge once @leeping acknowledges. |
|
I agree with all of your comments and we can proceed with the merge. There are certainly ways to accomplish the same thing with fewer dependencies that we should add in the future. |
This PR adds files and scripts for creating a liquid box and running a SMIRNOFF simulation on it, starting from just a SMILES string for a single molecule of the liquid. Example included for ethanol.