1# Solvated 5-mer peptide 2 3#---------------------------------- 4# Taken as is from examples/peptide 5 6units real 7atom_style full 8boundary p p p 9 10pair_style lj/charmm/coul/long 8.0 10.0 10.0 11bond_style harmonic 12angle_style charmm 13dihedral_style charmm 14improper_style harmonic 15kspace_style pppm 0.0001 16 17read_data data.peptide 18 19neighbor 2.0 bin 20neigh_modify delay 5 21 22timestep 2.0 23#---------------------------------- 24 25 26# temperature schedule for REMD 27variable idx world 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 28variable t world 200.0 209.0 219.0 230.0 241.0 252.0 264.0 276.0 289.0 303.0 317.0 332.0 348.0 365.0 382.0 400.0 29 30# thermostat 31fix thermostat all langevin $t $t 1000 772530 32 33# log-file output before minimization 34thermo_style custom step temp ke pe 35thermo 20 36 37# minimization 38minimize 1e-4 0.0 1000 1000 39 40# change logfile output after minimization 41thermo_style custom step temp pe 42thermo 20 43 44# trajectory style 45dump myDump all atom 20 peptide.${idx}.lammpstrj.gz 46dump_modify myDump sort id scale no 47 48# run REMD (for realistic results run for 100000000 steps with 10000 frequency) 49reset_timestep 0 50temper 2000 10 $t thermostat 3847 5382 51