updates on some comments

freeenergylab · Aug 29, 2024 · b7fb655 · b7fb655
1 parent cc7a6f5
commit b7fb655
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/abfe/abfe_alchemy_md.py b/abfe/abfe_alchemy_md.py
@@ -145,7 +145,7 @@ def _parse_args():
         )
     boresch_grp.add_argument(
         '-dc', '--dihedral_const', default=100.0, type=float,
-        help='Force constant for dihedral restraint, in kcal/mol'
+        help='Force constant for dihedral restraint, in kcal/mol/radian^2'
         )
     boresch_grp.add_argument(
         '-rs', '--restraint_seed', type=int, default=None,
@@ -843,4 +843,4 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs
                     _, out, _ = ctools.command_caller(command=shcmd, shell=True)
                     jobid = re.findall(r"job (.*?)\n", str(out))
                     with open('slurm_jobid.log', 'w') as f:
-                        f.writelines(f'INFO: ARRAY JOB ID {jobid[0]}')
+                        f.writelines(f'INFO: ARRAY JOB ID {jobid[0]}')
diff --git a/testing/abfe_testing/config.yaml b/testing/abfe_testing/config.yaml
@@ -74,7 +74,7 @@
         },
         "bond_const": 10.0,                               # force constant for Boresch-style bond restraint, in kcal/mol/A^2
         "angle_const": 100.0,                             # force constant for Boresch-style angle restraint, in kcal/mol/radian^2
-        "dihedral_const": 100.0,                          # force constant for Boresch-style dihedral restraint, in kcal/mol
+        "dihedral_const": 100.0,                          # force constant for Boresch-style dihedral restraint, in kcal/mol/radian^2
         "abfe_solvated_vdw_lambdas": [                    # lambda windows for solvated decoupled leg
             0.0, 0.05, 0.10, 0.15, 0.20,
             0.25, 0.30, 0.35, 0.40, 0.45,

diff --git a/testing/ahfe_testing/config.yaml b/testing/ahfe_testing/config.yaml
@@ -74,7 +74,7 @@
         },
         "bond_const": 10.0,                               # force constant for Boresch-style bond restraint, in kcal/mol/A^2
         "angle_const": 100.0,                             # force constant for Boresch-style angle restraint, in kcal/mol/radian^2
-        "dihedral_const": 100.0,                          # force constant for Boresch-style dihedral restraint, in kcal/mol
+        "dihedral_const": 100.0,                          # force constant for Boresch-style dihedral restraint, in kcal/mol/radian^2
         "abfe_solvated_vdw_lambdas": [                    # lambda windows for solvated decoupled leg
             0.0, 0.05, 0.10, 0.15, 0.20,
             0.25, 0.30, 0.35, 0.40, 0.45,