# PMF Input script template
# (1) Initialisation
units real
atom_style full
boundary p p p
pair_style hybrid/overlay lj/charmm/coul/long 10.0 12.0 buck/coul/long 12.0 morse 10.0
bond_style harmonic
angle_style harmonic
dihedral_style charmm
kspace_style pppm 0.0001
# (2) Define atoms
read_data c1.topo
group molecule molecule 1
group substrate molecule 2
group bottom molecule 3
# (3) Settings
# freeze bottom layer of substrate to prevent it from drifting
fix 2 bottom setforce 0 0 0
include new_defpot.pot
include best_all.pot
neighbor 2.0 bin
neigh_modify delay 0
timestep 1.0
# (4) NVT Dynamics
fix temp1 molecule nvt temp _TEMP_ _TEMP_ 100
fix temp2 substrate nvt temp _TEMP_ _TEMP_ 100
velocity                        all create _TEMP_ 293288
fix PMF molecule recenter NULL _Y_ NULL
compute temp_molecule molecule temp
compute yforce molecule group/group substrate kspace yes
thermo_style custom time c_yforce[2] etotal pe c_temp_molecule temp ke evdwl press enthalpy
thermo_modify flush yes
thermo 50
dump xyz all xyz 100000000 mol_sub.xyz
dump_modify xyz element C C H C N K Cl
dump coord all dcd 5000 trajectory.dcd
restart _NSTEPS_ TCB_PMF.restart
run _NSTEPS_