#system for LAMMPS simulation units real #dis=A, time=fs, energy=kcal/mol atom_style full log md.log # For a single processor calculation variable T equal 309 variable salt equal 240.0 # Salt concentration [mM] # Random number seed for Langevin integrator variable seed equal 18423 # Specify the different interaction styles bond_style class2 angle_style hybrid harmonic stacking/3spn2 dihedral_style 3spn2 # pair_stype 3spn2 [dna type] [temperature] [salt concentration (mM)] [short range cutoff] [Coulombic cutoff] pair_style hybrid/overlay 3spn2 bdna ${T} ${salt} 18.0 50.0 # Periodic boundary conditions boundary p p p # Turn on Newton's 2nd law newton on #yes # Read in the configuration read_data conf_lmp.in # Specify the pair coefficients pair_coeff 1 1 3spn2 0.239006 4.500000 pair_coeff 2 2 3spn2 0.239006 6.200000 pair_coeff 3 3 3spn2 0.239006 5.400000 pair_coeff 4 4 3spn2 0.239006 7.100000 pair_coeff 5 5 3spn2 0.239006 4.900000 pair_coeff 6 6 3spn2 0.239006 6.400000 pair_coeff 7 7 3spn2 0.239006 5.400000 pair_coeff 8 8 3spn2 0.239006 7.100000 pair_coeff 9 9 3spn2 0.239006 4.900000 pair_coeff 10 10 3spn2 0.239006 6.400000 pair_coeff 11 11 3spn2 0.239006 5.400000 pair_coeff 12 12 3spn2 0.239006 7.100000 pair_coeff 13 13 3spn2 0.239006 4.900000 pair_coeff 14 14 3spn2 0.239006 6.400000 pair_modify mix arithmetic pair_coeff 1*18 15*18 none # Zeroing out other interactions # Specify parameters for the neighbor list neighbor 4.0 multi neigh_modify check yes # A timestep of 0.02 ps timestep 20.0 # Initialize velocities from a Gaussian distribution velocity all create ${T} ${seed} rot yes mom yes dist gaussian # Calculating the different components of the non-bonded energy compute edna all pair 3spn2 variable ebp equal c_edna[1] # Base pairing energy variable ecstk equal c_edna[2] # Cross stacking energy variable eexcl equal c_edna[3] # Excluded volume energy variable dna_ecoul equal c_edna[4] # DNA coulombic energy variable nbp equal c_edna[5] # Number of base pairs # Specifying the frequency of thermodynamic output thermo 5000 thermo_style custom step v_nbp ebond eangle edihed v_ebp v_ecstk v_eexcl v_dna_ecoul temp # Specifying a Langevin integrator to perform a simulation in the NVT ensemble fix 1 all langevin ${T} ${T} 500 ${seed} gjf yes #Tstart Tstop damp fix 2 all nve # Write configuration to file # dump 1 all xyz 2000 main_test.xyz # Write configuration to file group sub type 3:14 dump mydump all custom 5000 traj.lammpstrj id type x y z # Run X number of steps run 1300000000