Merge branch 'main' into cbt

config.toml

@@ -94,146 +94,4 @@ kappa = 0.05
 sigma = 0.5
 # Interaction matrix, chi, ((atom name 1, atom name 2), (mixing energy in
 # [kJ/mol])).
-chi = [
-    # Don't need to specify 0 value interactions
-    # Here I assume all BB beads to be glycines
-    # inter BB-BB, set to zero
-    # BB - water
-    [["PBB", "W"], [-1.1]],
-    [["RBB", "W"], [-1.1]],
-    [["WBB", "W"], [-1.1]],
-    [["GBB", "W"], [-1.1]],
-    [["C", "W"], [42.24]], # Taken from DPPC
-    [["PBB", "CL"], [-1.1]],
-    [["RBB", "CL"], [-1.1]],
-    [["WBB", "CL"], [-1.1]],
-    [["GBB", "CL"], [-1.1]],
-    [["C", "CL"], [42.24]], # Taken from DPPC
-    # SC - water 
-    [["PSC", "W"], [-1.0]],
-    [["RSC", "W"], [-2.2]],
-    [["WSC1", "W"], [23.1]],
-    [["WSC2", "W"], [23.1]],
-    [["WSC3", "W"], [23.1]],
-    [["WSC4", "W"], [23.1]],
-    [["PSC", "CL"], [-1.0]],
-    [["RSC", "CL"], [-2.2]],
-    [["WSC1", "CL"], [23.1]],
-    [["WSC2", "CL"], [23.1]],
-    [["WSC3", "CL"], [23.1]],
-    [["WSC4", "CL"], [23.1]],
-    # SC - SC
-    [["PSC", "RSC"], [-3.4]],
-    [["PSC", "WSC1"], [-7.9]],
-    [["PSC", "WSC2"], [-7.9]],
-    [["PSC", "WSC3"], [-7.9]],
-    [["PSC", "WSC4"], [-7.9]],
-    [["RSC", "WSC1"], [-1.8]],
-    [["RSC", "WSC2"], [-1.8]],
-    [["RSC", "WSC3"], [-1.8]],
-    [["RSC", "WSC4"], [-1.8]],
-    # SC - BB
-    [["PSC", "RBB"], [-2.6]],
-    [["PSC", "WBB"], [-2.6]],
-    [["PSC", "GBB"], [-2.6]],
-    [["RSC", "PBB"], [-3.9]],
-    [["RSC", "WBB"], [-3.9]],
-    [["RSC", "GBB"], [-3.9]],
-    [["WSC1", "PBB"], [-5.0]],
-    [["WSC1", "RBB"], [-5.0]],
-    [["WSC1", "GBB"], [-5.0]],
-    [["WSC2", "PBB"], [-5.0]],
-    [["WSC2", "RBB"], [-5.0]],
-    [["WSC2", "GBB"], [-5.0]],
-    [["WSC3", "PBB"], [-5.0]],
-    [["WSC3", "RBB"], [-5.0]],
-    [["WSC3", "GBB"], [-5.0]],
-    [["WSC4", "PBB"], [-5.0]],
-    [["WSC4", "RBB"], [-5.0]],
-    [["WSC4", "GBB"], [-5.0]],
-    # Head - Tail
-    [["PBB", "C"], [5.0]],
-    [["RBB", "C"], [5.0]],
-    [["WBB", "C"], [5.0]],
-    [["GBB", "C"], [5.0]],
-    [["PSC", "C"], [5.0]],
-    [["RSC", "C"], [5.0]],
-    [["WSC1", "C"], [5.0]],
-    [["WSC2", "C"], [5.0]],
-    [["WSC3", "C"], [5.0]],
-    [["WSC4", "C"], [5.0]],
-]
-
-[bonds]
-# Two-particle bonds, ((atom name 1, atom name 2), (equilibrium length in
-# [nanometers], bond strength in [kJ/mol])). Note the two
-# Same for the angles since he used the combined angle-torsion potential.
-# IMPORTANT: numbers in arrays must have the same type!
-bonds = [
-  # Backbone
-  [["PBB", "RBB"], [0.35, 12500.0]],
-  [["RBB", "WBB"], [0.35, 12500.0]],
-  [["WBB", "GBB"], [0.35, 12500.0]],
-  [["GBB", "C"], [0.35, 12500.0]],
-  # [["GBB", "C"], [0.47, 1250.0]], # don't know which one is used from the itp
-  [["C", "C"], [0.47, 12500.0]],
-  # Sidechain
-  [["PBB", "PSC"], [0.30, 75000.0]],
-  [["RBB", "RSC"], [0.33, 50000.0]],
-  [["RSC", "RSC"], [0.34, 50000.0]],
-  [["WBB", "WSC1"], [0.30, 50000.0]],
-  # Check if this works, replacing elastic network
-  [["WSC1", "WSC2"], [0.27, 50000.0]],
-  [["WSC1", "WSC4"], [0.27, 50000.0]],
-  [["WSC2", "WSC3"], [0.27, 50000.0]],
-  [["WSC2", "WSC4"], [0.27, 50000.0]],
-  [["WSC3", "WSC4"], [0.27, 50000.0]],
-  [["WSC1", "WSC3"], [0.47, 50000.0]], # long diagonal, √3 * 0.27
-]
-# Three-particle angular bonds, ((atom name 1, atom name 2, atom name 3),
-# (equilibrium angle in [degrees], bond strength in [kJ/mol])
-angle_bonds = [
-  # Backbone - Sidechain
-  [["PSC", "PBB", "RBB"], [100.0, 25.0]],
-  [["PBB", "RBB", "RSC"], [100.0, 25.0]],
-  [["RBB", "WBB", "WSC1"], [100.0, 25.0]],
-  # [["RBB", "WBB", "WSC1"], [120.0, 25.0]],
-  # Sidechain
-  [["RBB", "RSC", "RSC"], [180.0, 25.0]],
-  [["WBB", "WSC1", "WSC4"], [90.0, 50.0]],
-  # [["WBB", "WSC1", "WSC2"], [210.0, 50.0]], # this one looks weird, why > 180?
-  [["WBB", "WSC1", "WSC2"], [150.0, 50.0]], # replaced the above one with this one
-  # Angles missing in martini topology, fixed by the elastic network
-  # [["WSC2", "WSC3", "WSC4"], [60.0, 50.0]],
-  # [["WSC2", "WSC1", "WSC4"], [60.0, 50.0]],
-  # [["WSC1", "WSC2", "WSC3"], [120.0, 50.0]],
-  # [["WSC2", "WSC4", "WSC3"], [120.0, 50.0]],
-  [["RSC", "RBB", "WBB"], [100.0, 25.0]],
-  [["WSC1", "WBB", "GBB"], [120.0, 25.0]],
-  # Tails
-  [["WBB", "GBB", "C"], [127.0, 20.0]],
-  [["GBB", "C", "C"], [180.0, 25.0]],
-  [["C", "C", "C"], [180.0, 25.0]],
-]
-# Four-particles torsion angles, the definition is as follows:
-# ((atom name 1, atom name 2, atom name 3, atom name 4),
-#  (coefficients), 
-#  (dihedral type))
-dihedrals = [
-  [
-    ["PBB", "RBB", "WBB", "GBB"],
-    [
-      [0],
-      [449.08790868, 610.2408724, -544.48626121, 251.59427866, -84.9918564], # c_k, kJ mol⁻¹ rad⁻²
-      # [224.54395434, 305.1204362, -272.24313061,  125.79713933, -42.4959282], # 50%
-      # [44.90879087, 61.02408724, -54.44862612, 25.15942787, -8.49918564], # 10%
-      [0.08, 0.46, 1.65, -0.96, 0.38], # d_k
-    ],
-    [1.0]
-  ],
-  # Impropers
-  [["WBB", "WSC2", "WSC4", "WSC1"], [0.0, 50.0], [2.0]],
-  [["WSC1", "WSC2", "WSC3", "WSC4"], [0.0, 200.0], [2.0]]
-  # Add improper dihedral for fixing W sidechain, the correct angle is needed
-  # "GBB", "RBB", "WBB", "WSC1"
-]
+chi = []

examples/config.toml

@@ -81,33 +81,33 @@ sigma = 0.5
 # Interaction matrix, chi, ((atom name 1, atom name 2), (mixing energy in
 # [kJ/mol])).
 chi = [
-  [["C", "W"], [42.24]],
-  [["G", "C"], [10.47]],
-  [["N", "W"], [-3.77]],
-  [["G", "W"],  [4.53]],
-  [["N", "P"], [-9.34]],
-  [["P", "G"],  [8.04]],
-  [["N", "G"],  [1.97]],
-  [["P", "C"], [14.72]],
-  [["P", "W"], [-1.51]],
-  [["N", "C"], [13.56]],
+  ["C", "W", 42.24],
+  ["G", "C", 10.47],
+  ["N", "W", -3.77],
+  ["G", "W",  4.53],
+  ["N", "P", -9.34],
+  ["P", "G",  8.04],
+  ["N", "G",  1.97],
+  ["P", "C", 14.72],
+  ["P", "W", -1.51],
+  ["N", "C", 13.56],
 ]
 
 [bonds]
 # Two-particle bonds, ((atom name 1, atom name 2), (equilibrium length in
 # [nanometers], bond strength in [kJ/mol])). Note the two
 bonds = [
-  [["N", "P"], [0.47, 1250.0]],
-  [["P", "G"], [0.47, 1250.0]],
-  [["G", "G"], [0.37, 1250.0]],
-  [["G", "C"], [0.47, 1250.0]],
-  [["C", "C"], [0.47, 1250.0]],
+  ["N", "P", 0.47, 1250.0],
+  ["P", "G", 0.47, 1250.0],
+  ["G", "G", 0.37, 1250.0],
+  ["G", "C", 0.47, 1250.0],
+  ["C", "C", 0.47, 1250.0],
 ]
 # Three-particle angular bonds, ((atom name 1, atom name 2, atom name 3),
 # (equilibrium angle in [degrees], bond strength in [kJ/mol])).
 angle_bonds = [
-  [["P", "G", "G"], [120.0, 25.0]],
-  [["P", "G", "C"], [180.0, 25.0]],
-  [["G", "C", "C"], [180.0, 25.0]],
-  [["C", "C", "C"], [180.0, 25.0]],
+  ["P", "G", "G", 120.0, 25.0],
+  ["P", "G", "C", 180.0, 25.0],
+  ["G", "C", "C", 180.0, 25.0],
+  ["C", "C", "C", 180.0, 25.0],
 ]