Write a standard polarisable OpenMM script (with polxml) + add directly the Tang-Toennis parameters inside (with coulttxml) #42
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For notation consistency, an "omm-p-tt.py" file is written instead of an "omm-p-sc.py" one. It prevent confusions with the "field-p-sc.py" file name, in which the "-sc" refers to the scaling of LJ parameters.
For notation consistency, an "omm-p-tt.py" file is written instead of an "omm-p-sc.py" one. It prevent confusions with the "field-p-sc.py" file name, in which the "-sc" refers to the scaling of LJ parameters.
agiliopadua
requested changes
Mar 5, 2025
coulttxml
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| print("OpenMM code for CoulTT written to addCoulTT.py") | ||
| if args.s is not None: | ||
| with open("omm-p-tt.py", 'w') as outputfile: | ||
| with open(args.s, 'r') as file: |
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Reading the omm-p.py script into data can be before and outside the 'with open("omm-p-tt.py")' structure, to avoid excessive indent
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| print("Tang-Toennis parameters written to omm-p-tt.py") | ||
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| elif args.s is None: |
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A lot of code is repeated. Can this be done in a more compact way?
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I condensed the code using a "write_coultt" function to avoid repetitions.
polxml
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| if data[line] == "### Run simulation ###\n": | ||
| del data[line:line+4] | ||
| outputfile.write("### Constants ###\n") |
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As in fftool, most of this is immutable text, so more suitable in a """..."""
Also, the question if this is the best way. Maybe include an omm-p.py example with polxml?
Scale with sqrt(k) when one fragment of dimer is already polarized. Make polarisable case-insensitive
Update scaleLJxml Scale with sqrt(k) when one fragment of dimer is already polarized. Make polarisable case-insensitive
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