#-----INITIALIZATION-----
units		real
atom_style	full
timestep 1.0
boundary p p p
#-----Force Fields-----
pair_style	lj/cut/coul/long 15.0 15.0
pair_modify	tail yes
bond_style	harmonic
angle_style	harmonic
improper_style cvff
kspace_style	pppm 1.0e-4
read_data	cyclopentanol.txt
replicate	5 5 4
variable dt equal dt
variable Tdamp equal 100.0*${dt}
variable Pdamp equal 100.0*${dt}
#-----Equilibriation-----
group	cyclopentanol type 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
neighbor 2.0 bin
neigh_modify delay 1 every 1 check no
velocity cyclopentanol create 300 13431343 dist uniform
#Reset the time step counter
reset_timestep  0                                    #Reset the time step counter to 0
fix		mynpt cyclopentanol npt temp 300.0 300.0 ${Tdamp} iso 1.0 1.0 ${Pdamp} mtk yes tloop 10 ploop 10

#Output Style
variable        Nevery equal 20                      #Specify the distance (in timesteps) between samples for computing ensemble aver$
                                                     #  (Interval between samples in a block)
variable        Nrepeat equal 50                     #Specify the number of samples per output  of thermodynamic averages
                                                     #  (Samples per block output)
variable        Nfreq equal ${Nevery}*${Nrepeat}     #Specify the dump interval (in timesteps)
                                                     #  (Some people call these blocks)
variable        PotentialEnergy equal epair          #Call the intermolecular potential energy $PotentialEnergy
variable        Pressure equal press                 #Call the pressure $Pressure
variable        Temperature equal temp               #Call the instantaneous temperature $Temperature
min_style	cg
minimize	0.0 0.0 2000 2000
compute myrdf cyclopentanol rdf 150 cutoff 15
fix             3 cyclopentanol ave/time ${Nevery} ${Nrepeat} ${Nfreq} v_Temperature v_PotentialEnergy v_Pressure file ave.out format %.8g  
fix				4 cyclopentanol ave/time ${Nevery} ${Nrepeat} ${Nfreq} c_myrdf[*] file tmp1.rdf mode vector
dump 5 cyclopentanol cfg 1 dump.equi_*.cfg mass type xs ys zs
dump_modify 5 element C1 C2 C3 C4 C5 O6 H7 H8 H9 H10 H11 H12 H13 H14 H15 H16
thermo          100                                 #Specify the interval between screen output of thermodynamic averages
#thermo  100
thermo_style    custom step temp epair ke etotal press #Format for screen output of thermodynamics
                                                     #  (MD step, temperature, internal energy, pressure)
#Run it!
run		110000
print "The end is near . . ."