# LAMMPS input file for RBC simulation, written by Hongyan Yuan & Ralph Kfoury, 2015 variable datafile string rbc_D50AA9m12_N21702_W_water_d0_water # Sets the variable name of the read data file used, change this name if the read data file name is changed variable P_damp equal 1 # Sets the Pressure damping variable used in the following " fix npt" commands variable P equal 0.05 # Sets the desired pressure of the system used in the following " fix npt" commands variable scale1 equal ramp(2.7,2.52) # Sets the scale performed in the final fix on water scaling down sigma from 2.7- 2.5 variable ew equal 0.2 # Sets the energy well ( epsilon) variable used in the pair coefficient specifications variable ini_T equal 0.02 # Sets the initial temperature used in the fix commands below variable T equal 0.23 # Sets the final temperature used in the fix commands below variable LD equal 1.0 # Sets the temperature damping parameter used in fix commands below variable fid string ${datafile} variable logfid string log.${fid} variable beta equal 0.0194*0.0 units lj # Sets the units used for the simulation, in this case: Lennard-Jones units #atom_style hybrid ellipsoid molecular # Defines the atom style used during the simulation, both ellipsoid and molecular. atom_style hybrid ellipsoid peri molecular bond_style harmonic1 # Sets the bond style as harmonic spring defined by Hooke's law boundary p p p # Creates the periodic boundaries of the simulation box read_data read_data.${datafile} # Specifies which read data file will be used to read in initial coordinates of system # spectrin bonds bond_coeff 1 50 1.5 # Defines the bond coefficients and spring constant for the spectrin network bonds # membrane-spectrin anchoring bond_coeff 2*3 20 2.0 # Defines the bond coefficients and spring constant for the transmembrane protein to spectrin network bonds mass * 1.0 set type 1*2 shape 1 1 1 # membrane particle are rigid body, it needs shape parameter to be set group bilayer type 1 2 # Creates a group called bilayer which consists of type 1 and 2 particles, #(Type 1 Bilayer, Type 2 Transmembrane proteins) group network type 3 4 5 # Creates a group called network which consists of type 3 4 5 particles group anchor_bonds type 2 3 5 group water_in type 6 # Creates a group called water_in consisting of type 6 particles ( Type 6 = Water inside Membrane) group water_out type 7 # Creates a group called water_out consisting of type 7 particles ( Type 7 = Water Outside Membrane) group water type 6 7 # Creates a group called water consisting of both type 6 and 7 particles ( Water inside + Out) velocity bilayer create ${T} 87287 loop geom # Creates Initial Velocity for bilayer particles ( Type 1 and 2) velocity network create ${ini_T} 87287 loop geom # Creates Initial Velocity for network particles ( Type 3 and 4 and 5) velocity water create ${T} 87287 loop geom # Creates Initial Velocity for water particles ( Type 6 and 7 ) pair_style hybrid lj/cut 3.6 fluidmembrane 2.6 # Sets the pair_style potentials used for the simulation, #in the case both lennard-jones/cut and the fluidmembrane potential pair_coeff 1*2 1*2 fluidmembrane 1.0 1.0 2.6 4 6 ${beta} # Sets the pair coefficients and parameters between type 1 and 2 (bilayer) particles pair_coeff 1*2 3*5 lj/cut ${ew} 1.0 # Sets the pair coefficients (Epsilon, Sigma) and parameters between type 1,2 (bilayer) and 3,4,5 ( Network Particles) pair_coeff 1*2 6*7 lj/cut ${ew} 1.0 # Sets the pair coefficients (Epsilon, Sigma) for interaction between type 1,2 (bilayer) and 6,7 (water) particles pair_coeff 3*5 3*5 lj/cut ${ew} 1.0 # Sets the pair coefficients (Epsilon, Sigma) for interaction between type 3,4,5 (network) # and type 3,4,5 (network) particles pair_coeff 3*5 6*7 lj/cut ${ew} 1.0 # Sets the pair coefficients (Epsilon, Sigma) for interaction between type 3,4,5 (network) # and type 6,7 (water) particles pair_coeff 6*7 6*7 lj/cut ${ew} 2.7 # Sets the pair coefficients (Epsilon, Sigma) for interaction between type 6,7 (water) # and type 6,7 (water) particles neighbor 1.0 bin thermo_style custom step temp press ebond # Printing thermodynamic data to the screen and log file thermo 200 # Sets the number of timesteps to run before printing out thermodynamic data timestep 0.005 # Sets the timestep of the simulation dump 1 all atom 500 dump.${fid}.${beta}.1.lammpstrj # Command sets when to dump a snapshot of atom quantities to one or # more files every N timesteps in one of several styles. ### equilibrium fix 1 water npt temp ${T} ${T} ${LD} iso ${P} ${P} ${LD} # Applies an NPT ensemble fix to the water group run 10000 fix 2 network npt temp ${ini_T} ${T} ${LD} iso ${P} ${P} ${P_damp} # Applies an NPT ensemble fix the network group using same parameters as above #fix 2 network nve #fix 2 network nvt temp ${ini_T} ${T} ${LD} run 20000 fix 3 bilayer nvt/asphere temp ${T} ${T} ${LD} # Applies an NVT (not NPT) ensemble fix to the network group using only temperature parameters #fix 3 bilayer nve/asphere #fix 3 bilayer nve run 10000 #fix 4 bilayer viscous 2.6 #fix 5 network viscous 32.5 ### change RBC volume fix 4 water adapt 1 pair lj/cut sigma 6 6 v_scale1 # Applies a final "adapt" fix to the water group and this will change the sigma value of LJ potential run 40000 unfix 4 run 20000