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minghao2016 · Apr 21, 2021 · 6e43d53 · 6e43d53
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diff --git a/reference/README → misc/reference/README b/reference/README → misc/reference/README
diff --git a/...ut_clean-cpHMD-GPU/constrain/1cvo_NPT.pdb → ...ut_clean-cpHMD-GPU/constrain/1cvo_NPT.pdb b/...ut_clean-cpHMD-GPU/constrain/1cvo_NPT.pdb → ...ut_clean-cpHMD-GPU/constrain/1cvo_NPT.pdb
diff --git a/...ce/input_clean-cpHMD-GPU/constrain/MD.mdp → ...ce/input_clean-cpHMD-GPU/constrain/MD.mdp b/...ce/input_clean-cpHMD-GPU/constrain/MD.mdp → ...ce/input_clean-cpHMD-GPU/constrain/MD.mdp
diff --git a/...nput_clean-cpHMD-GPU/constrain/analyse.py → ...nput_clean-cpHMD-GPU/constrain/analyse.py b/...nput_clean-cpHMD-GPU/constrain/analyse.py → ...nput_clean-cpHMD-GPU/constrain/analyse.py
diff --git a/...nput_clean-cpHMD-GPU/constrain/buffer.itp → ...nput_clean-cpHMD-GPU/constrain/buffer.itp b/...nput_clean-cpHMD-GPU/constrain/buffer.itp → ...nput_clean-cpHMD-GPU/constrain/buffer.itp
diff --git a/...input_clean-cpHMD-GPU/constrain/index.ndx → ...input_clean-cpHMD-GPU/constrain/index.ndx b/...input_clean-cpHMD-GPU/constrain/index.ndx → ...input_clean-cpHMD-GPU/constrain/index.ndx
diff --git a/...ce/input_clean-cpHMD-GPU/constrain/run.sh → ...ce/input_clean-cpHMD-GPU/constrain/run.sh b/...ce/input_clean-cpHMD-GPU/constrain/run.sh → ...ce/input_clean-cpHMD-GPU/constrain/run.sh
diff --git a/...input_clean-cpHMD-GPU/constrain/topol.top → ...input_clean-cpHMD-GPU/constrain/topol.top b/...input_clean-cpHMD-GPU/constrain/topol.top → ...input_clean-cpHMD-GPU/constrain/topol.top
diff --git a/.../input_clean-cpHMD-GPU/noconstrain/MD.mdp → .../input_clean-cpHMD-GPU/noconstrain/MD.mdp b/.../input_clean-cpHMD-GPU/noconstrain/MD.mdp → .../input_clean-cpHMD-GPU/noconstrain/MD.mdp
diff --git a/...n-cpHMD-GPU/noconstrain/MD_with_notes.mdp → ...n-cpHMD-GPU/noconstrain/MD_with_notes.mdp b/...n-cpHMD-GPU/noconstrain/MD_with_notes.mdp → ...n-cpHMD-GPU/noconstrain/MD_with_notes.mdp
diff --git a/...ut_clean-cpHMD-GPU/noconstrain/analyze.py → ...ut_clean-cpHMD-GPU/noconstrain/analyze.py b/...ut_clean-cpHMD-GPU/noconstrain/analyze.py → ...ut_clean-cpHMD-GPU/noconstrain/analyze.py
diff --git a/...ut_clean-cpHMD-GPU/noconstrain/buffer.itp → ...ut_clean-cpHMD-GPU/noconstrain/buffer.itp b/...ut_clean-cpHMD-GPU/noconstrain/buffer.itp → ...ut_clean-cpHMD-GPU/noconstrain/buffer.itp
diff --git a/...HMD-GPU/noconstrain/constant_ph_input.dat → ...HMD-GPU/noconstrain/constant_ph_input.dat b/...HMD-GPU/noconstrain/constant_ph_input.dat → ...HMD-GPU/noconstrain/constant_ph_input.dat
diff --git a/...put_clean-cpHMD-GPU/noconstrain/index.ndx → ...put_clean-cpHMD-GPU/noconstrain/index.ndx b/...put_clean-cpHMD-GPU/noconstrain/index.ndx → ...put_clean-cpHMD-GPU/noconstrain/index.ndx
diff --git a/...t_clean-cpHMD-GPU/noconstrain/protein.pdb → ...t_clean-cpHMD-GPU/noconstrain/protein.pdb b/...t_clean-cpHMD-GPU/noconstrain/protein.pdb → ...t_clean-cpHMD-GPU/noconstrain/protein.pdb
diff --git a/...ean-cpHMD-GPU/noconstrain/protein_NPT.pdb → ...ean-cpHMD-GPU/noconstrain/protein_NPT.pdb b/...ean-cpHMD-GPU/noconstrain/protein_NPT.pdb → ...ean-cpHMD-GPU/noconstrain/protein_NPT.pdb
diff --git a/.../input_clean-cpHMD-GPU/noconstrain/run.sh → .../input_clean-cpHMD-GPU/noconstrain/run.sh b/.../input_clean-cpHMD-GPU/noconstrain/run.sh → .../input_clean-cpHMD-GPU/noconstrain/run.sh
diff --git a/...put_clean-cpHMD-GPU/noconstrain/topol.top → ...put_clean-cpHMD-GPU/noconstrain/topol.top b/...put_clean-cpHMD-GPU/noconstrain/topol.top → ...put_clean-cpHMD-GPU/noconstrain/topol.top
diff --git a/...ut_legacy/benchmark/constant_ph_input.dat → ...ut_legacy/benchmark/constant_ph_input.dat b/...ut_legacy/benchmark/constant_ph_input.dat → ...ut_legacy/benchmark/constant_ph_input.dat
diff --git a/reference/input_legacy/benchmark/eq.gro → misc/reference/input_legacy/benchmark/eq.gro b/reference/input_legacy/benchmark/eq.gro → misc/reference/input_legacy/benchmark/eq.gro
diff --git a/reference/input_legacy/benchmark/md.mdp → misc/reference/input_legacy/benchmark/md.mdp b/reference/input_legacy/benchmark/md.mdp → misc/reference/input_legacy/benchmark/md.mdp
diff --git a/reference/input_legacy/benchmark/topol.top → ...eference/input_legacy/benchmark/topol.top b/reference/input_legacy/benchmark/topol.top → ...eference/input_legacy/benchmark/topol.top
diff --git a/...t_legacy/multistate/constant_ph_input.dat → ...t_legacy/multistate/constant_ph_input.dat b/...t_legacy/multistate/constant_ph_input.dat → ...t_legacy/multistate/constant_ph_input.dat
diff --git a/reference/input_legacy/multistate/eq.gro → .../reference/input_legacy/multistate/eq.gro b/reference/input_legacy/multistate/eq.gro → .../reference/input_legacy/multistate/eq.gro
diff --git a/reference/input_legacy/multistate/index.ndx → ...ference/input_legacy/multistate/index.ndx b/reference/input_legacy/multistate/index.ndx → ...ference/input_legacy/multistate/index.ndx
diff --git a/reference/input_legacy/multistate/md.mdp → .../reference/input_legacy/multistate/md.mdp b/reference/input_legacy/multistate/md.mdp → .../reference/input_legacy/multistate/md.mdp
diff --git a/reference/input_legacy/multistate/topol.top → ...ference/input_legacy/multistate/topol.top b/reference/input_legacy/multistate/topol.top → ...ference/input_legacy/multistate/topol.top
diff --git a/...e/input_legacy/orig/constant_ph_input.dat → ...e/input_legacy/orig/constant_ph_input.dat b/...e/input_legacy/orig/constant_ph_input.dat → ...e/input_legacy/orig/constant_ph_input.dat
diff --git a/reference/input_legacy/orig/eq.gro → misc/reference/input_legacy/orig/eq.gro b/reference/input_legacy/orig/eq.gro → misc/reference/input_legacy/orig/eq.gro
diff --git a/reference/input_legacy/orig/index.ndx → misc/reference/input_legacy/orig/index.ndx b/reference/input_legacy/orig/index.ndx → misc/reference/input_legacy/orig/index.ndx
diff --git a/reference/input_legacy/orig/md.mdp → misc/reference/input_legacy/orig/md.mdp b/reference/input_legacy/orig/md.mdp → misc/reference/input_legacy/orig/md.mdp
diff --git a/reference/input_legacy/orig/mdout.mdp → misc/reference/input_legacy/orig/mdout.mdp b/reference/input_legacy/orig/mdout.mdp → misc/reference/input_legacy/orig/mdout.mdp
diff --git a/reference/input_legacy/orig/run.tpr → misc/reference/input_legacy/orig/run.tpr b/reference/input_legacy/orig/run.tpr → misc/reference/input_legacy/orig/run.tpr
diff --git a/reference/input_legacy/orig/topol.top → misc/reference/input_legacy/orig/topol.top b/reference/input_legacy/orig/topol.top → misc/reference/input_legacy/orig/topol.top
diff --git a/...put_legacy/orig_new/constant_ph_input.dat → ...put_legacy/orig_new/constant_ph_input.dat b/...put_legacy/orig_new/constant_ph_input.dat → ...put_legacy/orig_new/constant_ph_input.dat
diff --git a/old/README b/old/README
diff --git a/old/analysis.py b/old/analysis.py
diff --git a/old/arrhenius.py b/old/arrhenius.py
diff --git a/old/cal/GlyAspGly.pdb b/old/cal/GlyAspGly.pdb
diff --git a/old/cal/GlyGluGly.pdb b/old/cal/GlyGluGly.pdb
diff --git a/old/cal/calibrate.py b/old/cal/calibrate.py
diff --git a/old/cal/fit.py b/old/cal/fit.py
diff --git a/old/cal/go.sh b/old/cal/go.sh
diff --git a/old/cal/initials.txt b/old/cal/initials.txt
diff --git a/old/cal/phbuilder.py b/old/cal/phbuilder.py