read_data	${fname}
read_data	yeastconf2.txt
  orthogonal box = (-14.608 -14.608 -14.608) to (14.608 14.608 14.608)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1602 atoms
  scanning bonds ...
  16 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  1599 bonds
  reading angles ...
  1567 angles
  16 = max # of 1-2 neighbors
  32 = max # of 1-3 neighbors
  64 = max # of 1-4 neighbors
  80 = max # of special neighbors



neighbor 2.0 multi


include interactions
bond_style  harmonic

special_bonds fene
  16 = max # of 1-2 neighbors
  16 = max # of special neighbors
bond_coeff 1 350.00 1.00
bond_coeff 2 350.00 1.80
bond_coeff 3 350.00 1.00
bond_coeff 4 350.00 1.00
bond_coeff 5 350.00 2.60
bond_coeff 6 350.00 1.80
bond_coeff 7 350.00 1.80
bond_coeff 8 350.00 1.00
bond_coeff 9 350.00 1.00
bond_coeff 10 350.00 1.00
bond_coeff 11 10.00 3.98

pair_style lj/cut 2.98
pair_modify shift yes
pair_coeff 1 1  1.00 1.00 1.15
pair_coeff 1 2  1.00 1.00 1.15
pair_coeff 1 3  1.00 1.80 2.07
pair_coeff 1 4  1.00 1.00 1.15
pair_coeff 1 5  0.00 1.00 1.15
pair_coeff 2 2  1.00 1.00 1.15
pair_coeff 2 3  1.00 1.80 2.07
pair_coeff 2 4  1.00 1.00 1.15
pair_coeff 2 5  0.00 1.00 1.15
pair_coeff 3 3  1.00 2.60 2.98
pair_coeff 3 4  1.00 1.80 2.07
pair_coeff 3 5  0.00 1.00 1.15
pair_coeff 4 4  1.00 1.00 1.15
pair_coeff 4 5  0.00 1.00 1.15
pair_coeff 5 5  0.00 1.00 1.15

angle_style  harmonic

angle_coeff 1  0.5 180
angle_coeff 2  0.0 180
angle_coeff 3  0.5 180
angle_coeff 4  0.5 180
angle_coeff 5  0.0 180
angle_coeff 6  0.0 180
angle_coeff 7  0.0 180
angle_coeff 8  0.5 180
angle_coeff 9  0.5 180
angle_coeff 10  0.5 180
angle_coeff 11  0.0 180
angle_coeff 12  0.0 180
angle_coeff 13  0.0 180
angle_coeff 14  0.0 180
angle_coeff 15  0.0 180
angle_coeff 16  0.0 180
angle_coeff 17  0.5 180
angle_coeff 18  0.5 180
angle_coeff 19  0.5 180
angle_coeff 20  0.5 180
include variables

#########################################################
#initialisation variable
variable rad equal 20.45
variable mrad equal 20.45

#Physical parameter

variable sigDna equal 1.00
variable isigDna equal 1.00
variable sigrDNA equal 2.60
variable isigrDNA equal 0.39

variable frad equal 13.28    #Radius of the nucleus


#lj sigma parameter of the repulsif interation between the nucleus and DNA
variable eNorm equal 1.0
variable sigNorm equal ${sigDna}/2.
variable sigNorm equal 1/2.
#Cutoff set to 1.12 this value; we keep only the repulsive part
variable sigNormCut equal ${sigNorm}*1.12
variable sigNormCut equal 0.5*1.12


#lj sigma parameter of the repulsif interation between the nucleus and DNA
variable eRibo equal 1.0
variable sigRibo equal ${sigrDNA}/2.
variable sigRibo equal 2.6/2.
#Cutoff set to 1.12 this value; we keep only the repulsive part
variable sigRiboCut equal ${sigRibo}*1.12
variable sigRiboCut equal 1.3*1.12

#Parameter of the attractive interaction between telomers and nucleus
variable etelo equal 4.00
variable sigtelo equal 2.00*${sigDna}
variable sigtelo equal 2.00*1
variable cuttelo equal 6.00*${sigDna}
variable cuttelo equal 6.00*1

#Damping
variable damp equal 2.0


#####################################################
# Equilibration (Langevin dynamics at 5000 K)

group telo type 2
32 atoms in group telo
group norm type 1 2 4 6
1451 atoms in group norm
group ribo type 3
150 atoms in group ribo
group centro type 4
16 atoms in group centro
group spb  type 5
1 atoms in group spb
group particle type 1 2 3 4 6
1601 atoms in group particle
#compute hic particle pair/local dist
#compute hicp particle property/local patom1 patom2



dump 		init all dcd 1000 dump_init.yeast.comp.dcd



###########################################################
#Definiton of nucleus and its interaction
#the telomere part is added when the nuceus has the right size

variable rad equal ${frad}
variable rad equal 13.28

region mySphere sphere 0.0 0.0 0.0 v_rad side in

fix wall1 norm wall/region mySphere lj126 ${eNorm} ${sigNorm} ${sigNormCut}
fix wall1 norm wall/region mySphere lj126 1 ${sigNorm} ${sigNormCut}
fix wall1 norm wall/region mySphere lj126 1 0.5 ${sigNormCut}
fix wall1 norm wall/region mySphere lj126 1 0.5 0.56
fix wall2 ribo wall/region mySphere lj126 ${eRibo} ${sigRibo} ${sigRiboCut}
fix wall2 ribo wall/region mySphere lj126 1 ${sigRibo} ${sigRiboCut}
fix wall2 ribo wall/region mySphere lj126 1 1.3 ${sigRiboCut}
fix wall2 ribo wall/region mySphere lj126 1 1.3 1.456
fix wall telo wall/region mySphere  lj93  ${etelo} ${sigtelo} ${cuttelo}
fix wall telo wall/region mySphere  lj93  4 ${sigtelo} ${cuttelo}
fix wall telo wall/region mySphere  lj93  4 2 ${cuttelo}
fix wall telo wall/region mySphere  lj93  4 2 6


velocity 	particle create 1.0 1231
fix		1 particle nve/limit 0.0005
fix		2 particle langevin 1.0 1.0 ${damp} 904297
fix		2 particle langevin 1.0 1.0 2 904297
run 10000
Memory usage per processor = 8.17265 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0   0.99937539 3.1855374e+10    118.90581 3.1855374e+10 8.1854598e+09 
   10000 0.0099696261    0.5223751   0.65390821    1.1912284   0.16205841 
Loop time of 5.88216 on 1 procs (1 MPI x 1 OpenMP) for 10000 steps with 1602 atoms

Pair  time (%) = 2.04133 (34.7038)
Bond  time (%) = 1.91556 (32.5656)
Neigh time (%) = 0.0109582 (0.186296)
Comm  time (%) = 0.00285244 (0.0484931)
Outpt time (%) = 0.000859499 (0.014612)
Other time (%) = 1.91059 (32.4812)

Nlocal:    1602 ave 1602 max 1602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    32590 ave 32590 max 32590 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 32590
Ave neighs/atom = 20.3433
Ave special neighs/atom = 1.99625
Neighbor list builds = 4
Dangerous builds = 0

unfix 1

thermo_style	custom step temp
thermo          10000
fix		1 particle nve/limit 0.05
timestep	0.005
run		100000
Memory usage per processor = 8.17265 Mbytes
Step Temp 
   10000 0.0099696261 
   20000    1.0053238 
   30000    1.0361092 
   40000    1.0194751 
   50000   0.97804215 
   60000   0.99038108 
   70000   0.99264421 
   80000    0.9961458 
   90000   0.98958888 
  100000    1.0034975 
  110000    1.0100775 
Loop time of 49.595 on 1 procs (1 MPI x 1 OpenMP) for 100000 steps with 1602 atoms

Pair  time (%) = 11.6489 (23.488)
Bond  time (%) = 18.9573 (38.2241)
Neigh time (%) = 4.54262 (9.15942)
Comm  time (%) = 0.0548093 (0.110514)
Outpt time (%) = 0.0127008 (0.025609)
Other time (%) = 14.3788 (28.9924)

Nlocal:    1602 ave 1602 max 1602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    23697 ave 23697 max 23697 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 23697
Ave neighs/atom = 14.7921
Ave special neighs/atom = 1.99625
Neighbor list builds = 1647
Dangerous builds = 0


write_data final.xyz



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

Please see the log.cite file for references relevant to this simulation

