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dynamics testing

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This commit is contained in:
Steve Plimpton
2022-04-12 12:54:23 -06:00
parent 8aa4c5a0e2
commit 01864189c7
5 changed files with 19 additions and 18 deletions
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5
examples/amoeba/in.ubiquitin
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@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit pitorsions PiTorsions & fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions fix bit bitorsions BiTorsions
pair_style amoeba pair_style amoeba include angle
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes special_bonds lj/coul 0.5 0.5 0.5 one/five yes
@ -39,10 +39,11 @@ special_bonds lj/coul 0.5 0.5 0.5 one/five yes
compute virial all pressure NULL virial compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp & thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal #press c_virial[*] emol etotal press c_virial[*]
# zero step run # zero step run
dump 1 all custom 10 dump.ubi id type x y z fx fy fz
run 0 run 0
# dynamics # dynamics

8
examples/amoeba/in.water_box.amoeba
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@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
# zero step run # zero step run
run 0 #run 0
# dynamics # dynamics
#thermo 1 thermo 1
#fix 1 all nve fix 1 all nve
#run 100 run 100

8
examples/amoeba/in.water_box.hippo
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@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
# zero step run # zero step run
run 0 #run 0
# dynamics # dynamics
#thermo 1 thermo 1
#fix 1 all nve fix 1 all nve
#run 100 run 100

8
examples/amoeba/in.water_dimer.amoeba
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@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
# zero step run # zero step run
run 0 #run 0
# dynamics # dynamics
#thermo 1 thermo 1
#fix 1 all nve fix 1 all nve
#run 100 run 100

8
examples/amoeba/in.water_dimer.hippo
View File

@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
# zero step run # zero step run
run 0 #run 0
# dynamics # dynamics
#thermo 1 thermo 1
#fix 1 all nve fix 1 all nve
#run 100 run 100