more mg

Author: carlocamilloni

src/multiego/ensemble.py

@@ -848,7 +848,7 @@ def generate_OO_LJ(meGO_ensemble):
         if atomtype == "O" or atomtype == "OM" or atomtype == "OA"
     ]
     H_H_sbtype = [sbtype for sbtype, atomtype in meGO_ensemble["sbtype_type_dict"].items() if atomtype == "H"]
-    N_sbtype = [sbtype for sbtype, atomtype in meGO_ensemble["sbtype_type_dict"].items() if atomtype == "N"]
+    N_sbtype = [sbtype for sbtype, atomtype in meGO_ensemble["sbtype_type_dict"].items() if atomtype == "N" or atomtype == "NT" or atomtype == "NL" or atomtype == "NR" or atomtype == "NZ" or atomtype == "NE"]
 
     full_matrix_OH = list(itertools.product(H_H_sbtype, O_OM_OA_sbtype)) + list(itertools.product(O_OM_OA_sbtype, H_H_sbtype))
     full_matrix_ON = list(itertools.product(N_sbtype, O_OM_OA_sbtype)) + list(itertools.product(O_OM_OA_sbtype, N_sbtype))

src/multiego/resources/type_definitions.py

@@ -6,11 +6,11 @@
 mg_eps = 0.11
 mg_eps_ho = 0.13
 mg_sig_ho = 0.1782 
-mg_eps_no = 0.10
+mg_eps_no = 0.13
 mg_sig_no = 0.2673 
 mg_eps_ch3 = 0.130
 mg_eps_ch2 = 0.120
-mg_eps_ch1 = 0.09
+mg_eps_ch1 = 0.100
 
 # Dataframe with GROMOS atom types and associated parameters
 gromos_atp = pd.DataFrame(
@@ -72,7 +72,7 @@
             1.0000000e-06 / 1.27911 * mg_eps_ch1,  # "O",
             7.4149321e-07 / 1.72504 * mg_eps_ch1,  # "OM",
             1.5055290e-06 / 0.84961 * mg_eps_ch1,  # "OA",
-            2.3195290e-06 / 0.63980 * mg_eps,  # "N",
+            2.3195290e-06 / 0.63980 * mg_eps_ch1,  # "N",
             5.0625000e-06 / 0.29314 * mg_eps_ch1,  # "NT",
             2.3195290e-06 / 0.63980 * mg_eps_ch1,  # "NL",
             3.3892810e-06 / 0.43786 * mg_eps_ch1,  # "NR",
@@ -98,7 +98,7 @@
             0.0022619536 / 1.27911 * mg_eps_ch1,  # "O",
             0.0022619536 / 1.72504 * mg_eps_ch1,  # "OM",
             0.0022619536 / 0.84961 * mg_eps_ch1,  # "OA",
-            0.0024364096 / 0.63980 * mg_eps,  # "N",
+            0.0024364096 / 0.63980 * mg_eps_ch1,  # "N",
             0.0024364096 / 0.29314 * mg_eps_ch1,  # "NT",
             0.0024364096 / 0.63980 * mg_eps_ch1,  # "NL",
             0.0024364096 / 0.43786 * mg_eps_ch1,  # "NR",