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add README for tinker2lmp.py

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Steve Plimpton
2022-04-18 16:52:34 -06:00
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Examples of how this tool created the data files in the
examples/amoeba directory:
** water_dimer:
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo
** water_hexamer:
% python tinker2lmp.py -xyz water_hexamer.xyz -amoeba amoeba_water.prm -data data.water_hexamer.amoeba
% python tinker2lmp.py -xyz water_hexamer.xyz -hippo hippo_water.prm -data data.water_hexamer.hippo
** water_box:
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643
** ubiquitin:
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new