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lammps/examples/amoeba
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Steve Plimpton dbcc08ba00 more refactoring for memory usage
2022-05-17 16:26:53 -06:00
..
amoeba_ubiquitin.key
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
amoeba_ubiquitin.prm
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
amoeba_water_box.key
new key files for water box example
2022-04-08 15:00:54 -06:00
amoeba_water.key
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
amoeba_water.prm
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
bitorsion.ubiquitin.data
reading of bitorsion data file
2022-03-14 18:08:14 -06:00
Compare.sh
refactoring edits
2022-05-17 14:40:09 -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
dump.ubi
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.ubi.1
test scripts
2022-05-17 12:44:11 -06:00
dump.ubi.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.ubi.32
test scripts
2022-05-17 12:44:11 -06:00
dump.ubi.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_box.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_box.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_box.amoeba.32
test scripts
2022-05-17 12:44:11 -06:00
dump.water_box.amoeba.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_box.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_box.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_box.hippo.32
test scripts
2022-05-17 12:44:11 -06:00
dump.water_box.hippo.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_dimer.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_dimer.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_dimer.amoeba.4
test scripts
2022-05-17 12:44:11 -06:00
dump.water_dimer.amoeba.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_dimer.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_dimer.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_dimer.hippo.4
test scripts
2022-05-17 12:44:11 -06:00
dump.water_dimer.hippo.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_hexamer.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_hexamer.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_hexamer.amoeba.4
test scripts
2022-05-17 12:44:11 -06:00
dump.water_hexamer.amoeba.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_hexamer.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
dump.water_hexamer.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
dump.water_hexamer.hippo.4
test scripts
2022-05-17 12:44:11 -06:00
dump.water_hexamer.hippo.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
hippo_water_box.key
new key files for water box example
2022-04-08 15:00:54 -06:00
hippo_water.key
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
hippo_water.prm
initial version of AMOEBA/HIPPO force field files
2021-08-25 13:53:31 -06:00
in.ubiquitin
test scripts
2022-05-17 12:44:11 -06:00
in.ubiquitin.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_box.amoeba
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_box.amoeba.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_box.hippo
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_box.hippo.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_dimer.amoeba
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_dimer.amoeba.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_dimer.hippo
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_dimer.hippo.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_hexamer.amoeba
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_hexamer.amoeba.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_hexamer.hippo
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
in.water_hexamer.hippo.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.ubi.1
test scripts
2022-05-17 12:44:11 -06:00
log.ubi.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.ubi.32
test scripts
2022-05-17 12:44:11 -06:00
log.ubi.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_box.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_box.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_box.amoeba.32
test scripts
2022-05-17 12:44:11 -06:00
log.water_box.amoeba.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_box.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_box.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_box.hippo.32
test scripts
2022-05-17 12:44:11 -06:00
log.water_box.hippo.32.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_dimer.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_dimer.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_dimer.amoeba.4
test scripts
2022-05-17 12:44:11 -06:00
log.water_dimer.amoeba.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_dimer.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_dimer.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_dimer.hippo.4
test scripts
2022-05-17 12:44:11 -06:00
log.water_dimer.hippo.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_hexamer.amoeba.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_hexamer.amoeba.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_hexamer.amoeba.4
test scripts
2022-05-17 12:44:11 -06:00
log.water_hexamer.amoeba.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_hexamer.hippo.1
test scripts
2022-05-17 12:44:11 -06:00
log.water_hexamer.hippo.1.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
log.water_hexamer.hippo.4
test scripts
2022-05-17 12:44:11 -06:00
log.water_hexamer.hippo.4.test
more refactoring for memory usage
2022-05-17 16:26:53 -06:00
README
tweak to README
2022-04-20 09:43:14 -06:00
Test.sh
test scripts
2022-05-17 12:44:11 -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 by the tools/tinker/tinker2lmp.py script

** 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