# Created by charmm2lammps v1.6.2 on Fri Jun  3 14:07:02 MDT 2005

units            real
dimension        3
atom_style       full
boundary         p p f
neighbor         2.0 bin
neigh_modify     delay 0 every 1 check yes
restart          25000 restart1 restart2
#read_restart    restart1 
read_data        mix.data          
##################################################   ################################################

pair_style      lj/charmm/coul/long 9.5 10.0 
                                         
pair_coeff      1 1   0.055   3.5500  #ca
.
.
.
pair_coeff      10 10   0.0000   0.0000  #hint

pair_modify     mix arithmetic

bond_style      harmonic

bond_coeff      1 517.00 1.5100
.
.
.
bond_coeff      10 320.00 1.4100

angle_style     harmonic

angle_coeff     1 60.00 109.50
.
.
. 
angle_coeff     16 50.00 109.50      

dihedral_style  opls

dihedral_coeff  1  0.0 7.25 0.0 0.0
.
.
. 
dihedral_coeff  26  0.65 -0.25 0.67 0.0

           
kspace_style    ewald 1.0e-4
kspace_modify   slab 3.0 mesh 1 1 1
special_bonds   charmm angle yes dihedral yes

####################################################     #####################################

group           water type 4 7
group           GO type 1 2 3 5 6
################################################  ########################################################################################

fix             1 all shake 0.0001 20 0 m 15.999400 b 3 a 6  
fix             2 GO setforce 0.0 0.0 NULL
fix             mom all momentum 1 linear 0 0 1 
compute          temp_water all temp
compute          peress all stress/atom
compute          press_water all pressure temp_water
velocity        water create 230.0 35281345 rot yes dist gaussian
fix             3 all npt temp 230.0 230.0 100.0 x 0.986923267 0.986923267 1000 y 0.986923267 0.986923267 1000  
fix_modify      3 press press_water temp temp_water
##################################################   ####################################################
timestep        1.0
################################################# etotal water ################################################
compute         1 water pe/atom
compute         2 water ke/atom
compute         3 water reduce sum c_1 c_2
variable        a equal c_3[1]
variable        b equal c_3[2]
fix             4 water print 1000 "$a" file pe.txt screen no
fix             5 water print 1000 "$b" file ke.txt screen no
variable        c equal v_a+v_b
#variable        d equal v_c/1152
fix             6 water ave/time 1 100 100 v_c file etotw.txt mode scalar
variable	      etot equal etotal
fix             7 all ave/time 1 100 100 v_etot file etot.txt mode scalar
variable	      temp equal temp
fix             tempreture all print 5000 "${temp}"  file temprature.txt screen no
thermo          500
thermo_style    custom step pe temp press   
##################################### density  ###########################################

compute         maxx water reduce max x 
compute         minx water reduce min x 
variable        sumx  equal c_maxx-c_minx
fix             lx water print 100 "${sumx}" file lx1.txt screen no
compute         maxy water reduce max y 
compute         miny water reduce min y 
variable        sumy  equal c_maxy-c_miny
fix             ly water print 100 "${sumy}" file ly1.txt screen no
compute         maxz water reduce max z 
compute         minz water reduce min z
variable        sumz  equal c_maxz-c_minz
fix             lz water print 100 "${sumz}" file lz1.txt screen no
variable        vol equal v_sumx*v_sumy*v_sumz  
fix             volume all print 100 "${vol}" file volume.txt screen no
variable        mass  equal mass(water)/6.0221367e+23
variable              density  equal v_mass/v_vol/1.0e-24
fix             8 water ave/time 1 100 100 v_density file density.txt mode scalar
####################################################  ##############################################
variable 	     p equal press
fix             pressure all print 5000 "${p}"  file pressure.txt screen no
#variable 	     lz equal lz
#fix             boxlengthz all print 1000 "${lz}"  file boxlengthz.txt screen no
#variable 	     ly equal ly
#fix             boxlengthy all print 1000 "${ly}"  file boxlengthy.txt screen no
#variable 	     lx equal lx
#fix             boxlengthx all print 1000 "${lx}"  file boxlengthx.txt screen no
variable 	     pxx equal press
fix             pressx all print 5000 "${pxx}"  file pressurex.txt screen no
variable 	     pyy equal press
fix             pressy all print 5000 "${pyy}"  file pressurey.txt screen no
variable 	     pzz equal press
fix             pressz all print 5000 "${pzz}"  file pressurez.txt screen no

fix             densz water ave/spatial 1 1000 10000 z -10 0.1 density/number file densz.profile

########## ### ########### #### ################ #### #############################################
dump             2 all xyz 50000 dump.all.xyz
dump_modify      2 element C1 C2 H3 H4 O5 O6 O7 O8 O9 H10
dump             4 water xyz 50000 dump.water.xyz
dump_modify      4 element C1 C2 H3 H4 O5 O6 O7 O8 O9 H10
dump             5 all custom 50000 dump.water.lammpstrj id type x y z 
run 20000000  #5ns