Merge pull request #6 from freeenergylab/dev

updates for revision
freeenergylab · Jan 8, 2025 · c835f37 · c835f37
2 parents 9d37b66 + 6364609
commit c835f37
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Showing 7 changed files with 11 additions and 23 deletions.
diff --git a/abfe/const.py b/abfe/const.py
@@ -24,10 +24,12 @@
 
 PRO_DEFS = {
     'ff14SB': {'source': 'leaprc.protein.ff14SB'},
+    'ff19SB': {'source': 'leaprc.protein.ff19SB'},
     }
 
 PHOSAA_DEFS = {
     'phosaa14SB': {'source': 'leaprc.phosaa14SB'},
+    'phosaa19SB': {'source': 'leaprc.phosaa19SB'},
     }
 
 LIPID_DEFS = {

diff --git a/testing/abfe_testing/config.yaml b/testing/abfe_testing/config.yaml
@@ -29,7 +29,7 @@
     },
     "topology": {
         "protein_name": "181L",                           # user-defined protein name
-        "protein_ff": "ff14SB",                           # {"ff14SB"}
+        "protein_ff": "ff14SB",                           # {"ff14SB", "ff19SB"}
         "ligand_ff": "gaff2",                             # {"gaff2"}
         "cofactor_names": [],                             # list of strings, e.g. ["CFA", "CFB"]
         "cofactor_ff": "gaff2",                           # {"gaff2"}
@@ -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": True,                                      # False: Turn off HMR; True: turn on HMR; for alchemy_md stage
+        "hmr": False,                                     # 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": 0.004,                                # in ps; 0.004 ps if HMR
+        "timestep": 0.002,                                # 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": 10.,                              # set force constant of positional restraint, in kcal/mol/A^2
     },
     "alchemy_morph": {
-        "hmr": True,                                      # False: Turn off HMR; True: turn on HMR; for alchemy_md stage
+        "hmr": False,                                     # 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": 0.004,                                # in ps; 0.004 ps if HMR
+        "timestep": 0.002,                                # 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
diff --git a/testing/abfe_testing/dG_results.csv b/testing/abfe_testing/dG_results.csv
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": True,                                      # False: Turn off HMR; True: turn on HMR; for equilibration stage
+        "hmr": False,                                     # False: Turn off HMR; True: turn on HMR; for equilibration stage
         "hmass": 3.024,                                   # hydrogen mass, in amu
     },
     "equilibration": {
         "dry_run": True,                                  # False: submit; True: only slurm bash script
-        "timestep": 0.004,                                # in ps; 0.004 ps if HMR
+        "timestep": 0.002,                                # 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": 10.,                              # set force constant of positional restraint, in kcal/mol/A^2
     },
     "alchemy_morph": {
-        "hmr": True,                                      # False: Turn off HMR; True: turn on HMR; for equilibration stage
+        "hmr": False,                                     # False: Turn off HMR; True: turn on HMR; for equilibration stage
         "hmass": 3.024,                                   # hydrogen mass, in amu
     },
     "alchemy_md": {
         "dry_run": True,                                  # False: submit; True: only slurm bash script
-        "timestep": 0.004,                                # in ps; 0.004 ps if HMR
+        "timestep": 0.002,                                # 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
diff --git a/testing/ahfe_testing/dG_results.csv b/testing/ahfe_testing/dG_results.csv