# Solvated 5-mer peptide

#---------------------------------- 
# Taken as is from examples/peptide 

units		    real
atom_style	    full
boundary        p p p 

pair_style	    lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style	pppm 0.0001

read_data	    data.peptide

neighbor	    2.0 bin
neigh_modify	delay 5

timestep	    2.0
#----------------------------------


# temperature schedule for REMD
variable        idx world 0     1     2     3     4     5     6     7     8     9     10    11    12    13    14    15
variable        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

# thermostat
fix             thermostat all langevin $t $t 1000 772530

# log-file output before minimization
thermo_style	custom step temp ke pe
thermo		    20

# minimization
minimize        1e-4 0.0 1000 1000

# change logfile output after minimization
thermo_style	custom step temp pe
thermo		    20

# trajectory style
dump            myDump all atom 20 peptide.${idx}.lammpstrj.gz
dump_modify     myDump sort id scale no

# run REMD (for realistic results run for 100000000 steps with 10000 frequency) 
reset_timestep  0
temper          2000 10 $t thermostat 3847 5382