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lammps/examples/amoeba
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Steve Plimpton c817a495e7 tweak README files 2022-07-11 09:44:23 -06:00
..
README tweak README files 2022-07-11 09:44:23 -06:00
amoeba_ubiquitin.key add metadata tags to the .key files too. 2022-07-05 11:20:15 -04:00
amoeba_ubiquitin.prm add UNITS: and DATA: metadata tags to force field files 2022-07-05 07:11:09 -04:00
amoeba_water.key add metadata tags to the .key files too. 2022-07-05 11:20:15 -04:00
amoeba_water.prm add UNITS: and DATA: metadata tags to force field files 2022-07-05 07:11:09 -04:00
amoeba_water_box.key add metadata tags to the .key files too. 2022-07-05 11:20:15 -04:00
bitorsion.ubiquitin.data reading of bitorsion data file 2022-03-14 18:08:14 -06:00
data.ubiquitin revert to original pitorsion code 2022-04-21 10:06:53 -06:00
data.water_box.amoeba recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
data.water_box.hippo recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
data.water_dimer.amoeba recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
data.water_dimer.hippo recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
data.water_hexamer.amoeba recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
data.water_hexamer.hippo recreate data files with different angle ordering method 2022-04-08 17:16:12 -06:00
hippo_water.key add metadata tags to the .key files too. 2022-07-05 11:20:15 -04:00
hippo_water.prm add UNITS: and DATA: metadata tags to force field files 2022-07-05 07:11:09 -04:00
hippo_water_box.key add metadata tags to the .key files too. 2022-07-05 11:20:15 -04:00
in.ubiquitin change length of ubi run 2022-07-07 15:02:48 -06:00
in.water_box.amoeba code tweaks and update of examples 2022-07-07 14:33:19 -06:00
in.water_box.hippo code tweaks and update of examples 2022-07-07 14:33:19 -06:00
in.water_dimer.amoeba code tweaks and update of examples 2022-07-07 14:33:19 -06:00
in.water_dimer.hippo code tweaks and update of examples 2022-07-07 14:33:19 -06:00
in.water_hexamer.amoeba code tweaks and update of examples 2022-07-07 14:33:19 -06:00
in.water_hexamer.hippo code tweaks and update of examples 2022-07-07 14:33:19 -06:00
log.7Jul22.ubiquitin.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.ubiquitin.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_box.amoeba.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_box.amoeba.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_box.hippo.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_box.hippo.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_dimer.amoeba.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_dimer.amoeba.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_dimer.hippo.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_dimer.hippo.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_hexamer.amoeba.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_hexamer.amoeba.g++.4 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_hexamer.hippo.g++.1 new log files 2022-07-07 15:01:55 -06:00
log.7Jul22.water_hexamer.hippo.g++.4 new log files 2022-07-07 15:01:55 -06:00
ubiquitin.xyz initial version of AMOEBA/HIPPO force field files 2021-08-25 13:53:31 -06:00
water_box.xyz initial version of AMOEBA/HIPPO force field files 2021-08-25 13:53:31 -06:00
water_dimer.xyz initial version of AMOEBA/HIPPO force field files 2021-08-25 13:53:31 -06:00
water_hexamer.xyz initial version of AMOEBA/HIPPO force field files 2021-08-25 13:53:31 -06:00

README 

Data files in this directory were created using the
tools/tinker/tinker2lmp.py script as follows:

** 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 -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data