From 01864189c76bd7e6e1b2f305026ff0cc65d22023 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 12 Apr 2022 12:54:23 -0600 Subject: [PATCH] dynamics testing --- examples/amoeba/in.ubiquitin | 5 +++-- examples/amoeba/in.water_box.amoeba | 8 ++++---- examples/amoeba/in.water_box.hippo | 8 ++++---- examples/amoeba/in.water_dimer.amoeba | 8 ++++---- examples/amoeba/in.water_dimer.hippo | 8 ++++---- 5 files changed, 19 insertions(+), 18 deletions(-) diff --git a/examples/amoeba/in.ubiquitin b/examples/amoeba/in.ubiquitin index d5fc3b0079..8870fcdf63 100644 --- a/examples/amoeba/in.ubiquitin +++ b/examples/amoeba/in.ubiquitin @@ -29,7 +29,7 @@ read_data data.ubiquitin fix amtype NULL "Tinker Types" & fix pit pitorsions PiTorsions & fix bit bitorsions BiTorsions -pair_style amoeba +pair_style amoeba include angle pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key 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 thermo_style custom step temp epair ebond eangle edihed eimp & - emol etotal #press c_virial[*] + emol etotal press c_virial[*] # zero step run +dump 1 all custom 10 dump.ubi id type x y z fx fy fz run 0 # dynamics diff --git a/examples/amoeba/in.water_box.amoeba b/examples/amoeba/in.water_box.amoeba index c15a684d95..3a37784f9d 100644 --- a/examples/amoeba/in.water_box.amoeba +++ b/examples/amoeba/in.water_box.amoeba @@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp & # zero step run -run 0 +#run 0 # dynamics -#thermo 1 -#fix 1 all nve -#run 100 +thermo 1 +fix 1 all nve +run 100 diff --git a/examples/amoeba/in.water_box.hippo b/examples/amoeba/in.water_box.hippo index df2f961b56..8e1d9a8e70 100644 --- a/examples/amoeba/in.water_box.hippo +++ b/examples/amoeba/in.water_box.hippo @@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp & # zero step run -run 0 +#run 0 # dynamics -#thermo 1 -#fix 1 all nve -#run 100 +thermo 1 +fix 1 all nve +run 100 diff --git a/examples/amoeba/in.water_dimer.amoeba b/examples/amoeba/in.water_dimer.amoeba index 05c2ff0584..c0e6ee35e4 100644 --- a/examples/amoeba/in.water_dimer.amoeba +++ b/examples/amoeba/in.water_dimer.amoeba @@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp & # zero step run -run 0 +#run 0 # dynamics -#thermo 1 -#fix 1 all nve -#run 100 +thermo 1 +fix 1 all nve +run 100 diff --git a/examples/amoeba/in.water_dimer.hippo b/examples/amoeba/in.water_dimer.hippo index 4ebe6d33ab..55b173b789 100644 --- a/examples/amoeba/in.water_dimer.hippo +++ b/examples/amoeba/in.water_dimer.hippo @@ -35,10 +35,10 @@ thermo_style custom step temp epair ebond eangle edihed eimp & # zero step run -run 0 +#run 0 # dynamics -#thermo 1 -#fix 1 all nve -#run 100 +thermo 1 +fix 1 all nve +run 100