diff --git a/testing/abfe_testing/config.yaml b/testing/abfe_testing/config.yaml index b4d1554..4828e0e 100644 --- a/testing/abfe_testing/config.yaml +++ b/testing/abfe_testing/config.yaml @@ -40,24 +40,24 @@ "com_box_buffer": 8.0, # box buffer for complex, in Angstrom "neutralize": True, # keep system neutral "ionconc": 0.15, # salt concentration, in Molar - "hmr": False, # False: Turn off HMR; True: turn on HMR; for equilibration stage + "hmr": True, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage "hmass": 3.024, # hydrogen mass, in amu }, "equilibration": { "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.002, # in ps; 0.004 ps if HMR - "solvated_length": 10., # simulation time for ligand in water, in ns - "complex_length": 10., # simulation time for ligand in binding pocket, in ns + "timestep": 0.004, # in ps; 0.004 ps if HMR + "solvated_length": 5., # simulation time for ligand in water, in ns + "complex_length": 5., # simulation time for ligand in binding pocket, in ns "restraintmask": "!:WAT,Cl-,K+,Na+ & !@H=", # specify solute heavy atoms for positional restraint during min-heat-press simulations, in Amber-Mask style - "restraint_wt": 5., # set force constant of positional restraint, in kcal/mol/A^2 + "restraint_wt": 10., # set force constant of positional restraint, in kcal/mol/A^2 }, "alchemy_morph": { - "hmr": False, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage + "hmr": True, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage "hmass": 3.024, # hydrogen mass, in amu }, "alchemy_md": { "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.002, # in ps; 0.004 ps if HMR + "timestep": 0.004, # in ps; 0.004 ps if HMR "remd": False, # True: turn on; False: turn off, replica-exchange method for FEP production simulation "remd_numexchg": 1000, # 1000 attempts for remd "solvated_length": 5.0, # FEP production simulation time for solvated leg, in ns diff --git a/testing/abfe_testing/dG_components_results.csv b/testing/abfe_testing/dG_components_results.csv index bd19c65..44eae69 100644 --- a/testing/abfe_testing/dG_components_results.csv +++ b/testing/abfe_testing/dG_components_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic -phn,5.20,0.00,5.16,0.00,9.72,0.00,-5.57,9.64,9.70,0.00,-6.27,9.64 +bnz,1.06,0.00,1.04,0.00,7.92,0.00,-6.11,9.57,7.75,0.00,-6.71,9.57 ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic -bnz,1.19,0.00,1.14,0.00,7.15,0.00,-6.72,9.58,7.06,0.00,-7.33,9.58 +phn,5.18,0.00,5.12,0.00,9.66,0.00,-6.06,9.61,9.74,0.00,-6.27,9.61 diff --git a/testing/abfe_testing/dG_results.csv b/testing/abfe_testing/dG_results.csv index 968083a..6a36f1e 100644 --- a/testing/abfe_testing/dG_results.csv +++ b/testing/abfe_testing/dG_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -phn,-0.45,0.06,-1.16,0.09 +bnz,-3.40,0.08,-3.85,0.10 ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -bnz,-3.11,0.06,-3.67,0.07 +phn,-0.94,0.10,-1.28,0.10 diff --git a/testing/ahfe_testing/config.yaml b/testing/ahfe_testing/config.yaml index ab9c97c..c6912f3 100644 --- a/testing/ahfe_testing/config.yaml +++ b/testing/ahfe_testing/config.yaml @@ -40,24 +40,24 @@ "com_box_buffer": 8.0, # box buffer for complex, in Angstrom "neutralize": True, # keep system neutral "ionconc": 0.15, # salt concentration, in Molar - "hmr": False, # False: Turn off HMR; True: turn on HMR; for equilibration stage + "hmr": True, # False: Turn off HMR; True: turn on HMR; for equilibration stage "hmass": 3.024, # hydrogen mass, in amu }, "equilibration": { - "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.002, # in ps; 0.004 ps if HMR - "solvated_length": 10., # simulation time for ligand in water, in ns - "complex_length": 10., # simulation time for ligand in binding pocket, in ns + "dry_run": True, # False: submit; True: only slurm bash script + "timestep": 0.004, # in ps; 0.004 ps if HMR + "solvated_length": 5., # simulation time for ligand in water, in ns + "complex_length": 5., # simulation time for ligand in binding pocket, in ns "restraintmask": "!:WAT,Cl-,K+,Na+ & !@H=", # specify solute heavy atoms for positional restraint during min-heat-press simulations, in Amber-Mask style - "restraint_wt": 5., # set force constant of positional restraint, in kcal/mol/A^2 + "restraint_wt": 10., # set force constant of positional restraint, in kcal/mol/A^2 }, "alchemy_morph": { - "hmr": False, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage + "hmr": True, # False: Turn off HMR; True: turn on HMR; for equilibration stage "hmass": 3.024, # hydrogen mass, in amu }, "alchemy_md": { - "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.002, # in ps; 0.004 ps if HMR + "dry_run": True, # False: submit; True: only slurm bash script + "timestep": 0.004, # in ps; 0.004 ps if HMR "remd": False, # True: turn on; False: turn off, replica-exchange method for FEP production simulation "remd_numexchg": 1000, # 1000 attempts for remd "solvated_length": 5.0, # FEP production simulation time for solvated leg, in ns diff --git a/testing/ahfe_testing/dG_components_results.csv b/testing/ahfe_testing/dG_components_results.csv index e83c27c..ccefb04 100644 --- a/testing/ahfe_testing/dG_components_results.csv +++ b/testing/ahfe_testing/dG_components_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc -bnz,1.13,0.00,1.12,0.00 +phn,5.08,0.00,4.99,0.00 ,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc -phn,5.24,0.00,5.20,0.00 +bnz,1.09,0.00,1.03,0.00 diff --git a/testing/ahfe_testing/dG_results.csv b/testing/ahfe_testing/dG_results.csv index 83ce369..32fd52b 100644 --- a/testing/ahfe_testing/dG_results.csv +++ b/testing/ahfe_testing/dG_results.csv @@ -1,4 +1,4 @@ ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -bnz,-1.13,0.04,-1.12,0.04 +phn,-5.08,0.06,-4.99,0.07 ,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -phn,-5.24,0.05,-5.20,0.05 +bnz,-1.09,0.05,-1.03,0.06