# LAMMPS input BER_MD units real boundary p p p newton on # use off for np>4 atom_style molecular # can use "full" if atoms have charges bond_style harmonic angle_style harmonic dihedral_style charmm #improper_style harmonic pair_style lj96/cut 12 read_data BER_premin.dat #read_restart BER_min.restart.702 # mapping of BER to LAMMPS atom types non bonded interactions: # 1 = BER; 2 = XYR; # pair_coeff i j eps (kcal/mol) sig (Angstrom) pair_coeff 1 1 0.2953 3.800 pair_coeff 1 2 0.3999 3.900 pair_coeff 2 2 0.5400 4.000 # scale NB interactions of bonded atoms special_bonds lj/coul 0.0 0.0 0.0 # neighbor list parameters (modify to ensure "Dangerous builds = 0" in log file) neighbor 5.0 bin neigh_modify delay 5 #compute temp1 all temp thermo_style custom step temp pe etotal spcpu vol press # add "vol" for constant NPT thermo 50 # constant NVT Nose-Hoover thermostat w/ 1 ps time constant # for constant NPT use "npt temp 298.0 298.0 1000.0 iso 1.0 1.0 5000.0" # (i.e. 5ps time constant for pressure) # NB: Marrink recommends Berendsen thermostat for MARTINI model # but Nose-Hoover is more physical fix constnpt all npt temp 298.0 298.0 1000.0 iso 1.0 1.0 5000.0 velocity all create 298.0 84143573 mom yes dist gaussian #fix atomrdf all rdf 100 file.rdf 250 1 1 2 2 3 3 4 4 5 5 1 2 1 3 dump atomdump all custom 1000 BER_MD.lammpstrj id type mol x y z ix iy iz # dump file for analysis dump atomdump2 all atom 1000 BER_MDv.lammpstrj # dump file for VMD viewing (optional) restart 10000 BER_MD.restart timestep 10 run 5000