Comments (2)
Also mostly duplicated: gmxprefix.bash and rungmx.sh
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Here's a bit from an email thread, to remind myself:
- Introduced a new method md() in gmxio.py. It is basically the
same as molecular_dynamics() but does not do the analysis, because
this will be different for the different quantities.Cool. This could possibly replace molecular_dynamics() at some
point - I was not completely happy with how it was doing the analysis
since it returns a set of chosen quantities. Related to item (2)
above, it might be helpful for the engine to have methods that
retrieve the time series such as mdtraj_potentials(), mdtraj_rhos()
or something.
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Related Issues (20)
- Close files after opening in Molecule HOT 2
- use_pvals option fails to work due to non-conversion to numpy array HOT 1
- Self-polarization correction does not work with Liquid_SMIRNOFF
- Liquid.pdb: Sizes detected: {3, 6} and the PBC
- Forcebalance fails to read some xyz files containing coordinates in scientific notation HOT 2
- Large values with Hessian target HOT 3
- (not urgent) single parameter optimization with workers fails HOT 1
- Compatibility with OpenMM-7.7.0 HOT 4
- I/O error when parsing Tinker Output HOT 3
- Computing FD gradient of angle with OpenMM 7.7.0
- Pymbar 4 compatibility HOT 3
- use openff-units for conversion factors (not urgent) HOT 2
- ForceBalance takes really long to complete HOT 2
- evaluator unit bug
- TypeError with ForceBalance-1.9.4 HOT 17
- runcuda.sh overwrites environment variables HOT 3
- Unexpected keyword argument 'return_topology' HOT 2
- ForceBalance is taking very long time over 1 day HOT 3
- Encountering error while attempting to fit ab initio data using GROMACS for periodic systems. HOT 1
- ValueError: could not convert string to float: 'Polarization'
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