fix: slow growth

launch.json

@@ -7,6 +7,13 @@
             "request": "launch",
             "program": "${workspaceFolder}/src/kimmdy/cmd.py",
             "cwd": "${workspaceFolder}/example/alanine_hat_naive/"
+        },
+        {
+            "name": "KIMMDY custom run",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/src/kimmdy/cmd.py",
+            "cwd": "${workspaceFolder}/../../examples/gly-hydrolysis/"
         }
     ]
 }

src/kimmdy/constants.py

@@ -19,6 +19,20 @@
     "dihedral_restraints": [0, 1, 2, 3],
 }
 
+# from gmx data dir
+DEFAULT_EDISSOC: dict[tuple[str, str], float] = { # type: ignore
+ tuple(sorted(list(k))): v for k, v in {
+    ("C", "N"): 500.0,
+    ("CA", "C"): 341.0,
+    ("CA", "N"): 379.0,
+    ("CA", "CB"): 400.0,
+    ("CB", "CG"): 400.0,
+    ("CG", "CD"): 400.0,
+    ("CD", "CE"): 400.0,
+    ("CE", "NZ"): 400.0
+}.items()
+}
+
 # see https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
 FFFUNC = {
     "mult_proper_dihedral": "9",