From 353ebb11f10efaf511cc57e01540be06ac6c553f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 18 Apr 2022 16:52:34 -0600 Subject: [PATCH] add README for tinker2lmp.py --- tools/tinker/README | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 tools/tinker/README diff --git a/tools/tinker/README b/tools/tinker/README new file mode 100644 index 0000000000..04ee066642 --- /dev/null +++ b/tools/tinker/README @@ -0,0 +1,26 @@ +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 + +