From 10815d57d1dd12827852b8d56d55b53a4002b0c3 Mon Sep 17 00:00:00 2001 From: Manuel Carrer Date: Tue, 12 Oct 2021 10:58:52 +0200 Subject: [PATCH] Update config file --- config.toml | 163 ++++++++++++++++++++++++------------------ examples/prot_15.toml | 19 ++--- 2 files changed, 106 insertions(+), 76 deletions(-) diff --git a/config.toml b/config.toml index 77e50475..104a27c1 100644 --- a/config.toml +++ b/config.toml @@ -1,14 +1,25 @@ # [meta] # Name of the simulation. May be ommitted. -# name = "Alanine octa-peptide in vacuum" +# name = "PRWG lipopeptide micelle in water" # Tags classifying the simulation. May be ommitted. -# tags = ["peptide", "ALA"] +# tags = ["lipopeptides", "PRWG"] + +# Here's the topology of a PRWG molecule +# +# WSC2 -- WSC3 +# | | +# PSC(+) WSC1 -- WSC4 +# | | +# PBB -- RBB -- WBB -- GBB -- C -- C -- C -- C +# | +# RSC -- RSC(+) +# [particles] # Number of total particles in the simulation. If an input .hdf5 format file is # specified, the number of particles will be inferred from this and *may* be # ommited here. -# n_particles = +n_particles = 11876 # specify number of ghost particles, used for dipole point charges in the CBT dihedral potential (default = 0) # n_ghots = 0 # Mass of the particles in [g/mol]. All masses are assumed equal. @@ -20,16 +31,17 @@ mass = 72.0 [simulation] # Number of total time steps in the simulation. -n_steps = 1000 # 6 ns +n_steps = 200 # Frequency of trajectory/energy file output in time steps. -n_print = 10 # 300 ps +n_print = 1 # Frequency of requesting that the HDF5 library flush the file output buffers # to disk after in number of n_print timesteps. n_flush = 10 # Time step used in the simulation in [picoseconds]. -time_step = 0.3 +time_step = 0.03 # Simulation box size in [nanometers]. box_size = [10.73911, 10.76184, 11.30546] +# box_size = [5.0, 5.0, 5.0] # for single PRWG molecule test # Time integrator used in the simulation. Either "velocity-verlet" or "respa". # If "respa", specify also the number of small rRESPA time steps per large # time_step with the 'respa_inner' keyword. @@ -39,17 +51,17 @@ respa_inner = 5 # reduce the amount of neccessary communication between ranks in the pmesh # procedures. Ommit or set to 'false' or '0' to not perform any domain # decomposition. -# domain_decomposition = 100 -domain_decomposition = 100 +domain_decomposition = 1000 +# domain_decomposition = false # Remove linear center of mass momentum from the system before integration # starts. cancel_com_momentum = true # Starting temperature to generate before simulation begins in [kelvin]. Ommit # or set to 'false' to not change the temperature before starting. -start_temperature = 330 +start_temperature = 300 # Target temperature used in the velocity rescale thermostat in [kelvin]. Ommit # or set to 'false' to use no thermostat, i.e. a constant energy simulation. -target_temperature = 330 +target_temperature = 300 # Thermostat collision frequency in [1/picoseconds]. tau = 1 # Couple groups of particles species to individual different thermostats. @@ -83,31 +95,34 @@ sigma = 0.5 # Interaction matrix, chi, ((atom name 1, atom name 2), (mixing energy in # [kJ/mol])). chi = [ - # Don't need to specify 0 terms - # [["PBB", "W"], [0.0]], - # [["RBB", "W"], [0.0]], - # [["WBB", "W"], [0.0]], - # [["GBB", "W"], [0.0]], - # water + # 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]], - [["C", "W"], [42.24]], # Taken from DPPC - # CL == water [["PSC", "CL"], [-1.0]], [["RSC", "CL"], [-2.2]], [["WSC1", "CL"], [23.1]], [["WSC2", "CL"], [23.1]], [["WSC3", "CL"], [23.1]], [["WSC4", "CL"], [23.1]], - [["C", "CL"], [42.24]], # Taken from DPPC - # inter BB-BB - # - # - # inter side-side + # SC - SC [["PSC", "RSC"], [-3.4]], [["PSC", "WSC1"], [-7.9]], [["PSC", "WSC2"], [-7.9]], @@ -117,36 +132,36 @@ chi = [ [["RSC", "WSC2"], [-1.8]], [["RSC", "WSC3"], [-1.8]], [["RSC", "WSC4"], [-1.8]], - # inter side-BB - [["PSC", "RBB"], [-3.4]], - [["PSC", "WBB"], [-7.9]], + # SC - BB + [["PSC", "RBB"], [-2.6]], + [["PSC", "WBB"], [-2.6]], [["PSC", "GBB"], [-2.6]], - [["RSC", "PBB"], [-3.4]], - [["RSC", "WBB"], [-1.8]], + [["RSC", "PBB"], [-3.9]], + [["RSC", "WBB"], [-3.9]], [["RSC", "GBB"], [-3.9]], - [["WSC1", "PBB"], [-7.9]], - [["WSC1", "RBB"], [-1.8]], + [["WSC1", "PBB"], [-5.0]], + [["WSC1", "RBB"], [-5.0]], [["WSC1", "GBB"], [-5.0]], - [["WSC2", "PBB"], [-7.9]], - [["WSC2", "RBB"], [-1.8]], + [["WSC2", "PBB"], [-5.0]], + [["WSC2", "RBB"], [-5.0]], [["WSC2", "GBB"], [-5.0]], - [["WSC3", "PBB"], [-7.9]], - [["WSC3", "RBB"], [-1.8]], + [["WSC3", "PBB"], [-5.0]], + [["WSC3", "RBB"], [-5.0]], [["WSC3", "GBB"], [-5.0]], - [["WSC4", "PBB"], [-7.9]], - [["WSC4", "RBB"], [-1.8]], + [["WSC4", "PBB"], [-5.0]], + [["WSC4", "RBB"], [-5.0]], [["WSC4", "GBB"], [-5.0]], - # inter head-tail - [["PBB", "C"], [15.0]], - [["RBB", "C"], [4.0]], - [["WBB", "C"], [4.0]], - [["GBB", "C"], [4.0]], - [["PSC", "C"], [15.0]], - [["RSC", "C"], [15.0]], - [["WSC1", "C"], [1.0]], - [["WSC2", "C"], [1.0]], - [["WSC3", "C"], [1.0]], - [["WSC4", "C"], [1.0]], + # 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] @@ -156,23 +171,24 @@ chi = [ # IMPORTANT: numbers in arrays must have the same type! bonds = [ # Backbone - [["PBB", "RBB"], [0.35, 1250.0]], - [["RBB", "WBB"], [0.35, 1250.0]], - [["WBB", "GBB"], [0.35, 1250.0]], - [["GBB", "C"], [0.35, 1250.0]], - # [["GBB", "C"], [0.47, 1250.0]], + [["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, 7500.0]], - [["RBB", "RSC"], [0.33, 5000.0]], - [["RSC", "RSC"], [0.34, 5000.0]], - [["WBB", "WSC1"], [0.30, 5000.0]], - # Check if this works, substituting elastic network - [["WSC1", "WSC2"], [0.27, 5000.0]], - [["WSC1", "WSC4"], [0.27, 5000.0]], - [["WSC2", "WSC3"], [0.27, 5000.0]], - [["WSC3", "WSC4"], [0.27, 5000.0]], - # Tails - [["C", "C"], [0.47, 1250.0]], + [["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]) @@ -181,15 +197,23 @@ angle_bonds = [ [["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"], [150.0, 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), @@ -199,9 +223,10 @@ dihedrals = [ [ ["PBB", "RBB", "WBB", "GBB"], [ - [0], # λ = 0 ==> random coil - # [44.91, 61.02, -54.45, 25.16, -8.50], # c_k, might need to scale this by 0.5 - [22.45439543, 30.51204362, -27.22431306, 12.57971393, -4.24959282], + [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] @@ -209,4 +234,6 @@ dihedrals = [ # 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" ] diff --git a/examples/prot_15.toml b/examples/prot_15.toml index ef683bc3..e64fe665 100644 --- a/examples/prot_15.toml +++ b/examples/prot_15.toml @@ -18,7 +18,7 @@ mass = 72.0 [simulation] # Number of total time steps in the simulation. -n_steps = 1000 +n_steps = 2000 # Frequency of trajectory/energy file output in time steps. n_print = 1 # Frequency of requesting that the HDF5 library flush the file output buffers @@ -32,12 +32,12 @@ box_size = [6.25, 6.25, 6.25] # If "respa", specify also the number of small rRESPA time steps per large # time_step with the 'respa_inner' keyword. integrator = "respa" -respa_inner = 5 +respa_inner = 10 # Perform MPI rank domain decomposition every x time steps to (hopefully) # reduce the amount of neccessary communication between ranks in the pmesh # procedures. Ommit or set to 'false' or '0' to not perform any domain # decomposition. -domain_decomposition = false +domain_decomposition = 1000 # Remove linear center of mass momentum from the system before integration # starts. cancel_com_momentum = true @@ -92,13 +92,14 @@ chi = [ # Same for the angles since he used the combined angle-torsion potential. # IMPORTANT: numbers in arrays must have the same type! bonds = [ - [["BB", "BB"], [0.38, 12500.0]], - [["BB", "SC"], [0.18, 12500.0]], + [["BB", "BB"], [0.38, 1250.0]], + [["BB", "SC"], [0.18, 5000.0]], ] # Three-particle angular bonds, ((atom name 1, atom name 2, atom name 3), # (equilibrium angle in [degrees], bond strength in [kJ/mol]) angle_bonds = [ - # [["BB", "BB", "SC"], [120.0, 25.0]], # β sheet + [["BB", "BB", "SC"], [120.0, 25.0]], # β sheet + [["BB", "BB", "SC"], [108.0, 25.0]], # α helix [["BB", "BB", "SC"], [108.0, 25.0]], # α helix ] # Four-particles torsion angles, the definition is as follows: @@ -154,8 +155,10 @@ dihedrals = [ [ ["BB", "BB", "BB", "BB"], [ - [-0.5], - [44.90879087, 61.02408724, -54.44862612, 25.15942787, -8.49918564], + [1], + # [0.13680, 0.18589, -0.16586, 0.07664, -0.02589], # c_k, kJ mol⁻¹ deg⁻² + [449.08790868, 610.2408724, -544.48626121, 251.59427866, -84.9918564], # c_k, kJ mol⁻¹ rad⁻² + # [44.90879087, 61.02408724, -54.44862612, 25.15942787, -8.49918564], [0.07700393, 0.46230281, 1.65322823, -0.9600009, 0.37807322], ], [1.0]