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