updated testing results

freeenergylab · Aug 13, 2024 · 2cc25d2 · 2cc25d2
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Showing 6 changed files with 24 additions and 24 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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