units           real

neigh_modify    delay 2 every 1

atom_style      full

bond_style      harmonic

angle_style     charmm

dihedral_style  charmm

improper_style  harmonic

pair_style lj/charmm/coul/long 8 10

pair_modify     mix arithmetic

kspace_style    pppm 1e-4

read_data       equi4_comb.data

group prot id 1:13910

group nterm id 5 896 1789 2243 2690 3140 4044 4930 5823 6032 6486 6933 7383 8287 9173 10066 10767 11214 11668 12125 13029
 
group cterm id 886 1777 2218 3128 4019 4910 5811 6461 6913 7371 8262 9153 10495 10742 11194 11648 12113 13004 13895

special_bonds   charmm

group NVT subtract all nterm

fix             1 NVT nvt temp 310 310 100 #iso 0 0 1000

variable mytime equal time 

if ${mytime}<=18000 then "variable vl equal -0.0005" else "variable vl equal 0.00"

#variable t equal "${vl}"

#fix 1 all nve

#fix             2 all shake 1e-6 500 0 m 1.0

#velocity        all create 0.0 12345678 dist uniform

compute atomstress prot stress/atom NULL

compute         allp prot reduce sum c_atomstress[1] c_atomstress[2] c_atomstress[3]

compute voro prot voronoi/atom


compute 22 prot reduce sum c_voro[1] c_voro[2]

variable        protpress equal -(c_allp[1]+c_allp[2]+c_allp[3])/(3*c_22[1])

compute 1 prot chunk/atom bin/1d x lower 0.00390625 units reduced

fix surf       prot ave/chunk 500 1 1000 1 density/mass density/number temp vx vy vz fx fy fz c_atomstress[1] c_atomstress[2] c_atomstress[3] c_voro[1] c_voro[2] file pull_coil_helix.surf

#fix 2 nterm rigid group 1 nterm

fix zeroforce nterm setforce  NULL 0 0

fix force cterm setforce 0 0 0
 
velocity nterm set NULL 0 0

fix 2 nterm rigid group 1 nterm

velocity cterm set 0 0 0

#fix ff nterm aveforce -15 0.0 0.0

fix  pull    nterm smd cvel 20.0 v_vl tether -195 NULL NULL 0

#fix  nopull    all rigid group 2 cterm nterm

#compute cc1 nterm chunk/atom molecule

compute myChunk nterm com

fix cck nterm ave/time 1000 1 1000 c_myChunk[*] file tmp.out mode vector

thermo          500

timestep       1

#restart         10 step1_pdbreader.restart1 step1_pdbreader.restart2

dump            1 all atom 2000 relax_comb.dump

dump_modify     1 image yes scale no

dump 2 nterm custom 1000 nterm.dump id type  x y z fx fy fz vx vy vz 

thermo_style  custom step time temp pe etotal evdwl ecoul epair ebond eangle edihed eimp emol press pxx pyy pzz vol f_pull[1] f_pull[2] f_pull[3] f_pull[4] f_pull[5] f_pull[6] f_pull[7] v_protpress 
 
run             20000

write_data rlx_comb.data

write_restart rlx_comb.restart

#unfix zeroforce
#fix zerof nterm setforce  0 0 0
#velocity nterm set 0 0 0
#unfix pull
#fix  pull    nterm smd cvel 20.0 0 tether -195 NULL NULL 0
#run 1000000
#write_data relax_comb4.data