diff --git a/1.Static/MASTERFILES/Init/Eq.5_1.N1000.data b/1.Static/MASTERFILES/Init/Eq.5_1.N1000.data
new file mode 100644
index 0000000000000000000000000000000000000000..48f31f3d4936c31d2cc99457d612146de643264e
--- /dev/null
+++ b/1.Static/MASTERFILES/Init/Eq.5_1.N1000.data
@@ -0,0 +1,4032 @@
+LAMMPS data file via write_data, version 12 Dec 2018, timestep = 0
+
+1000 atoms
+5 atom types
+1000 bonds
+2 bond types
+1000 angles
+1 angle types
+
+-8.0000000000000000e+01 8.0000000000000000e+01 xlo xhi
+-8.0000000000000000e+01 8.0000000000000000e+01 ylo yhi
+-8.0000000000000000e+01 8.0000000000000000e+01 zlo zhi
+
+Masses
+
+1 1
+2 1
+3 1
+4 1
+5 1
+
+Atoms # angle
+
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diff --git a/1.Static/MASTERFILES/Topo2_random_region.c++ b/1.Static/MASTERFILES/Topo2_random_region.c++
new file mode 100644
index 0000000000000000000000000000000000000000..66ca119d50d42340c7d84aac605c7e36059a2f61
--- /dev/null
+++ b/1.Static/MASTERFILES/Topo2_random_region.c++
@@ -0,0 +1,228 @@
+#include<iostream>
+#include<math.h>
+#include<stdlib.h>
+#include<fstream>
+#include<sstream>
+#include<vector>
+#include<ctime>
+#include <unistd.h>
+#include<functional>
+#include<numeric>
+#include<cstdlib>
+#include <algorithm>
+using namespace std;
+
+int Ntot,ntype;
+double Lmaxx,Lminx,Lmaxy,Lminy,Lmaxz,Lminz;
+double Lx,Ly,Lz;
+string dummy;
+int nangles,nangletypes,nbonds,nbondtypes;
+//
+int id,mol,type;
+double x,y,z;
+int ix,iy,iz;
+double vx,vy,vz;
+//
+const int N=1;
+const int Nbeads=1000;
+double Polymer[N][Nbeads][6]; //x,y,z,mol,type,id
+double PolymerWrap[N][Nbeads][3]; //x,y,z
+int PolymerImg[N][Nbeads][3]; //ix,iy,iz
+double Velocity[N][Nbeads][3];
+int Angles[Nbeads][4]; //bead1,bead2,bead3,atype
+int Bonds[Nbeads+1][3]; //bead1,bead2,btype
+
+
+double distance(double v1[6], double v2[6]);
+int main(int argc, char* argv[]){
+cout << " ############################# EXTERNAL LOOP TOPOII ################### " <<endl;
+
+//ARGV[1]=timestep
+//ARGV[2]=infile-no time
+//ARGV[3]=outfile-no time
+//ARGV[4]=Random seed
+int time=atoi(argv[1]);
+int seedr=atoi(argv[4]);
+
+
+
+//READ FILE
+ifstream indata;
+stringstream readFile;
+readFile.str("");
+readFile.clear();
+readFile << argv[2] << argv[1];
+indata.open(readFile.str().c_str());
+cout << readFile.str().c_str()<<endl;
+if(!indata.good()){cout << "Could not find file"<<endl; cin.get();cin.get();cin.get();}
+
+//read lines
+for(int i=0;i<12;i++){
+if(i==2) {
+indata >> Ntot;
+}
+if(i==3){
+indata >> ntype;
+}
+if(i==4){
+indata >> nbonds;
+}
+if(i==5){
+indata >> nbondtypes;
+}
+if(i==6){
+indata >> nangles;
+}
+if(i==7){
+indata >> nangletypes;
+}
+if(i==9) {
+indata >> Lminx >> Lmaxx;
+Lx = Lmaxx-Lminx;
+}
+if(i==10) {
+indata >> Lminy >> Lmaxy;
+Ly = Lmaxy-Lminy;
+}
+if(i==11) {
+indata >> Lminz >> Lmaxz;
+Lz = Lmaxz-Lminz;
+}
+else{
+getline(indata,dummy);
+}
+}
+
+while(1==1){
+getline(indata,dummy);
+string str=dummy;
+string str2 ("Atoms");
+if (str.find(str2) != string::npos)break;
+}
+
+//READ ATOMS
+for(int n=0; n<Ntot; n++){
+	indata >> id>> mol>>type>> x>>y>>z>>ix>>iy>>iz;
+	PolymerWrap[0][id-1][0]=x;
+	PolymerWrap[0][id-1][1]=y;
+	PolymerWrap[0][id-1][2]=z;
+	PolymerImg[0][id-1][0]=ix;
+	PolymerImg[0][id-1][1]=iy;
+	PolymerImg[0][id-1][2]=iz;
+	//
+	Polymer[0][id-1][0]=x+Lx*ix;
+	Polymer[0][id-1][1]=y+Ly*iy;
+	Polymer[0][id-1][2]=z+Lz*iz;
+	Polymer[0][id-1][3]=mol;
+	Polymer[0][id-1][4]=type;
+	Polymer[0][id-1][5]=id;
+}
+
+//READ VELOCITIES
+indata >> dummy;
+for(int n=0; n<Ntot; n++){
+	indata >> id >> vx>>vy>>vz;
+	Velocity[0][id-1][0]=vx;
+	Velocity[0][id-1][1]=vy;
+	Velocity[0][id-1][2]=vz;
+}
+
+//READ BONDS
+int nbonds0=Nbeads;
+int bid,btype,b1,b2;
+bid=0;btype=0;b1=0;b2=0;
+for(int n=0;n<nbonds;n++)for(int p=0;p<3;p++)Bonds[n][p]=0;
+indata >> dummy;
+for(int nb=0; nb<nbonds; nb++){
+	indata >> bid >> btype>>b1>>b2;
+	Bonds[bid-1][0]=b1;
+	Bonds[bid-1][1]=b2;
+	Bonds[bid-1][2]=btype;
+}
+
+//READ ANGLES
+int aid,atype,a1,a2,a3;
+aid=0;atype=0;a1=0;a2=0;a3=0;
+for(int na=0;na<nangles;na++)for(int pa=0;pa<4;pa++)Angles[na][pa]=0;
+indata >> dummy;
+for(int na=0; na<nangles; na++){
+	indata >> aid >> atype>>a1>>a2>>a3;
+	Angles[na][0]=a1;
+	Angles[na][1]=a2;
+	Angles[na][2]=a3;
+	Angles[na][3]=atype;
+}
+
+
+//////////////////
+///// TOPO 2 /////
+//////////////////
+//Created the topoII region only at the beggining of the simulation (timestep=0), after calling this programm from inside LAMMPS.
+//This is done by changing the type of particles in the topoII region to type 4.
+if(time==0){
+int loc;
+loc = rand() % Nbeads;
+
+int wtopo2=50;
+for (int i=0;i<wtopo2;i++){
+int j=(loc-wtopo2+i);
+if(j<0)j+=Nbeads;
+Polymer[0][j][4]=4;
+}
+}
+
+/////////////////////////////////////////////////////////////////////////
+///////////////////	WRITE NEW FILE  /////////////////////////////////////
+/////////////////////////////////////////////////////////////////////////
+
+//OUTFILE
+stringstream writeFile;
+writeFile <<argv[3]<<argv[1];
+ofstream write(writeFile.str().c_str());
+cout << "writing on .... " <<writeFile.str().c_str()<<endl;
+write.precision(19);
+write << "LAMMPS data file via write_data, version 15 May 2015, timestep = "<< argv[1]<< endl;
+write <<endl;
+write << Ntot  << " atoms "<<endl;
+write << ntype  << " atom types "<<endl;
+write << nbonds << " bonds "<<endl;
+write << nbondtypes << " bond types "<<endl;
+write << nangles << " angles "<<endl;
+write << nangletypes << " angle types "<<endl;
+write << "\n";
+write << Lminx << " " << Lmaxx << " xlo xhi"<<endl;
+write << Lminy << " " << Lmaxy << " ylo yhi"<<endl;
+write << Lminz << " " << Lmaxz << " zlo zhi"<<endl;
+write << "\nMasses \n"<<endl;
+for(int j=0; j<ntype;j++) write << j+1 << " " << 1<< endl;
+
+write << "\nAtoms \n"<<endl;
+for(int n=0; n<Ntot;n++) write << Polymer[0][n][5] << " " << Polymer[0][n][3] << " " <<  Polymer[0][n][4] << " " << PolymerWrap[0][n][0] << " " <<PolymerWrap[0][n][1] << " " << PolymerWrap[0][n][2] << " " << PolymerImg[0][n][0] << " " << PolymerImg[0][n][1] << " " << PolymerImg[0][n][2] << endl;
+
+
+write << "\n\n\nVelocities\n"<<endl;
+for(int n=0; n<Ntot;n++) write << n+1 << " " << Velocity[0][n][0] << " "<< Velocity[0][n][1] << " "<<  Velocity[0][n][2] << endl;
+
+
+write << "\nBonds \n"<<endl;
+for(int n=0; n<nbonds;n++) {
+write << n+1 << " " << Bonds[n][2] << " " << Bonds[n][0] << " " << Bonds[n][1] << endl;
+}
+
+write << "\nAngles \n"<<endl;
+for(int na=0; na<nangles;na++){
+write << na+1 << " " << Angles[na][3] << " " << Angles[na][0] << " " << Angles[na][1] << " " << Angles[na][2]<< endl;
+}
+cout << " ###################################### FIN ############################## " <<endl;
+
+return 0;
+
+}
+
+double distance(double v1[6], double v2[6]){
+double d=0;
+
+d=(v1[0]-v2[0])*(v1[0]-v2[0])+(v1[1]-v2[1])*(v1[1]-v2[1])+(v1[2]-v2[2])*(v1[2]-v2[2]);
+
+return sqrt(d);
+}
diff --git a/1.Static/MASTERFILES/run.lam b/1.Static/MASTERFILES/run.lam
new file mode 100644
index 0000000000000000000000000000000000000000..327450bd84abd2619bc786e55f403576b9f16047
--- /dev/null
+++ b/1.Static/MASTERFILES/run.lam
@@ -0,0 +1,234 @@
+####################################
+####	ULOOP			####
+####################################
+# These default settings are set such that the looping occours through the bash.run.sh script file.
+#jbn is the number of simulations
+variable jbn uloop 1
+variable startfrom equal 0
+variable jn equal ${jbn}+${startfrom}
+print ${jn}
+
+#################################
+####    PARAMETERS       ########
+#################################
+#file with the random seed variables (seedthermo, seedtopo, seed00 ) 
+include parameters.dat
+
+#temperature of the system
+variable Temp equal 1.0
+
+variable tdamp equal 1.0
+
+#Equilibration
+variable run1 equal 10000000
+
+#Run
+variable run2 equal 500000000
+
+#Restart every these timesteps
+variable trestart equal 10000000
+
+#Dump data every these timesteps
+variable dumpfreq equal 100000
+
+#Dump trajectory every these timesteps
+variable dumptraj equal 1000000
+
+################################
+####	DEFINTIONS 	    ########
+################################
+#Where the restart files of the run (non the equilibration) will be stored
+variable folder index DUMPS
+shell mkdir ${folder}
+
+#The starting configuration is always the same. Also the name of the restart files
+variable rname   index Init/Eq.5_1.N1000.data
+variable simname index Run.R${jn}
+
+units lj
+atom_style angle 
+boundary        p p p
+neighbor 1.4 bin
+neigh_modify every 1 delay 1 check yes 
+
+restart ${trestart} ${folder}/Restart.${simname}.
+read_data ${rname}
+
+####################################
+####	BOX AND WALL       #######
+####################################
+change_box all x final -80 80 y final -80 80 z final -80 80 boundary p p p units box
+#fix WALL all wall/lj126 xhi EDGE 1.0 1.0 1.122462048 xlo EDGE 1.0 1.0 1.122462048 yhi EDGE 1.0 1.0 1.122462048 ylo EDGE 1.0 1.0 1.122462048 zhi EDGE 1.0 1.0 1.122462048 zlo EDGE 1.0 1.0 1.122462048 units box
+
+####################################
+####	ANGLE	             #######
+####################################
+angle_style   cosine
+angle_coeff  1 5.0 #20 sigma for realistic DNA (1 bead = 2.5 nm)
+
+####################################
+####	PAIRS	             #######
+############################2########
+pair_style  lj/cut 1.12246
+pair_modify     shift yes
+pair_coeff	* * 1.0 1.0 1.12246
+
+###################################
+####  FENE	 ##################
+##################################
+bond_style   fene
+#It turns off the LJ part of the FENE-bond potential between 1-2 atoms. However, the pairwise LJ interaction is still on
+special_bonds fene#<=== I M P O R T A N T (new command).
+bond_coeff    1  30.0   1.6  1.0  1.0
+bond_coeff    2  30.0   1.6  1.0  1.0
+
+####################################
+####	THERMO AND INTEGRATION
+####################################
+thermo 1000000
+thermo_style   custom   step  temp  epair vol cpu
+timestep 0.01 
+
+####################################
+####    FIXES                #######
+####################################
+fix 1 all   nve
+fix 2 all  langevin   ${Temp} ${Temp} ${tdamp}  ${seedthermo}
+
+#Useful commands when running in parallel
+comm_style tiled
+fix bal all balance 10000 1.1 rcb
+comm_modify cutoff 3.0
+
+run ${run1}
+reset_timestep 0
+
+
+#########################################
+## WRITE RESTART AND ADDS TOPO II##
+#######################################
+#Where the restart (data) file after equilibration will be stored
+variable datafolder index Data
+shell mkdir ${datafolder}
+
+variable wname   index dataRestart.${simname}.
+variable newname index newdataRestart.${simname}.
+
+write_data ${wname}0
+
+#Run the program that takes the restart file and places the topo II 
+shell ./Topo2_random_region 0 ${wname} ${newname} ${seedtopo}
+shell mv ${wname}0 ${datafolder}/${wname}0
+
+
+
+
+
+
+
+
+
+
+##############################################################
+###  START RUN USING RESTART FILE WITH ADDED TOPO  ##
+##############################################################
+variable xyzname index XYZ_${simname}.xyz
+
+clear
+units lj
+atom_style angle 
+boundary        p p p
+neighbor 1.2 bin
+neigh_modify every 1 delay 1 check yes 
+
+
+variable rnewname index newdataRestart.${simname}.
+read_data ${rnewname}0
+shell mv ${rnewname}0 Data/${rnewname}0
+
+###############################
+####	BOX AND WALL	 ######
+###############################
+change_box all x final -80 80 y final -80 80 z final -80 80 boundary p p p  units box
+units box
+
+#######################################################
+####	PAIRS -- REPULSIVE + TOPO II 	#######
+#######################################################
+pair_style  hybrid lj/cut 1.12246 soft 1.12246
+pair_modify     shift yes
+pair_coeff      * * lj/cut 1.0 1.0 1.12246
+## NOW THERE IS TOPO2 -- TYPE 4 BEADS ARE SOFT AND CAN BE CROSSED
+pair_coeff      * 4 soft 2.0  1.12246
+pair_coeff      * 5 soft 20.0 1.12246
+
+
+####################################
+####	ANGLE	             #######
+####################################
+angle_style   cosine
+angle_coeff  1 5.0 #20 sigma for realistic DNA (1 bead = 2.5 nm)
+
+########################
+## PER PRIMI VICINI   ##
+########################
+bond_style fene
+#It turns off the LJ part of the FENE-bond potential between 1-2 atoms. However, the pairwise LJ interaction is still on
+special_bonds fene#<=== I M P O R T A N T (new command)
+bond_coeff   1 30.0   1.6  1.0  1.0
+bond_coeff   2 30.0   1.6  1.0  1.0
+
+####################################
+####	DUMPS	             #######
+####################################
+dump 2 all custom ${dumpfreq} ${folder}/${simname}.* id type x y z ix iy iz
+dump_modify 2 sort id
+
+##XYZ
+dump 4 all xyz ${dumptraj} ${xyzname}
+dump_modify 4 element O N Ca P Au
+
+####################################
+####	FIXES	             #######
+####################################
+timestep 0.01
+fix 1 all   nve  
+fix 2 all  langevin   ${Temp} ${Temp} ${tdamp}   ${seed00}
+
+#Useful commands when running in parallel
+comm_style tiled
+fix bal all balance 10000 1.1 rcb
+comm_modify cutoff 3.0
+
+thermo 10000
+thermo_style   custom step  temp  epair ebond eangle vol cpu
+run ${run2} 
+################################################
+
+################
+## ULOOP    ####
+################
+clear
+
+variable folder     delete
+variable rname      delete
+variable xyzname    delete
+variable simname    delete
+variable jn         delete
+variable wname      delete
+variable rnewname   delete
+variable newname    delete
+variable seedthermo delete
+variable seedtopo   delete
+variable seed00     delete
+
+next jbn
+jump SELF #last line!!!
+
+### If e.g. I run this on 10 partitions of 1 processor,
+### and initialise the variable with 'uloop N'
+### it will run 10 simulations with 'jobnumber' taking 
+### values 1-10. Then when a particular simulation finishes, the 
+### script will be run again with the next value of jobnumber, 
+### until N simulations have been run.
+## SO ULOOP IS "SERIAL" BUT FOR SURE 10x1 PROCs ARE ALWAYS BUSY
diff --git a/1.Static/MASTERFILES/run.lam.restart b/1.Static/MASTERFILES/run.lam.restart
new file mode 100644
index 0000000000000000000000000000000000000000..2ed0367adf6d9f6082943acce0dfc86ceecbdea4
--- /dev/null
+++ b/1.Static/MASTERFILES/run.lam.restart
@@ -0,0 +1,244 @@
+####################################
+####	ULOOP			####
+####################################
+# These default settings are set such that the looping occours through the bash.run.sh script file.
+#jbn is the number of simulations
+variable jbn uloop 1
+variable startfrom equal 0
+variable jn equal ${jbn}+${startfrom}
+print ${jn}
+
+
+###################################
+#### restart file and timestep ####
+###################################
+variable readingtime equal 100000000
+variable readingfile index Restart.topo2.${readingtime}
+
+
+#################################
+####    PARAMETERS       ########
+#################################
+#file with the random seed variables (seedthermo, seedtopo, seed00 ) 
+include parameters.dat
+
+#temperature of the system
+variable Temp equal 1.0
+
+variable tdamp equal 1.0
+
+#Equilibration
+variable run1 equal 0
+
+#Run
+variable run2 equal 500000000
+
+#Restart every these timesteps
+variable trestart equal 10000000
+
+#Dump data every these timesteps
+variable dumpfreq equal 100000
+
+#Dump trajectory every these timesteps
+variable dumptraj equal 1000000
+
+################################
+####	DEFINTIONS 	    ########
+################################
+#Where the restart files of the run (non the equilibration) will be stored
+variable folder index DUMPS
+shell mkdir ${folder}
+
+#The starting configuration is always the same. Also the name of the restart files
+variable rname   index Data/${readingfile}
+variable simname index Run.R${jn}
+
+units lj
+atom_style angle 
+boundary        p p p
+neighbor 1.4 bin
+neigh_modify every 1 delay 1 check yes 
+
+read_restart ${rname}
+
+####################################
+####	BOX AND WALL       #######
+####################################
+change_box all x final -101 101 y final -101 101 z final -101 101 boundary p p p units box
+#fix WALL all wall/lj126 xhi EDGE 1.0 1.0 1.122462048 xlo EDGE 1.0 1.0 1.122462048 yhi EDGE 1.0 1.0 1.122462048 ylo EDGE 1.0 1.0 1.122462048 zhi EDGE 1.0 1.0 1.122462048 zlo EDGE 1.0 1.0 1.122462048 units box
+
+####################################
+####	ANGLE	             #######
+####################################
+angle_style   cosine
+angle_coeff  1 5.0 #20 sigma for realistic DNA (1 bead = 2.5 nm)
+
+####################################
+####	PAIRS	             #######
+############################2########
+pair_style  lj/cut 1.12246
+pair_modify     shift yes
+pair_coeff	* * 1.0 1.0 1.12246
+
+###################################
+####  FENE	 ##################
+##################################
+bond_style   fene
+#It turns off the LJ part of the FENE-bond potential between 1-2 atoms. However, the pairwise LJ interaction is still on
+special_bonds fene#<=== I M P O R T A N T (new command).
+bond_coeff    1  30.0   1.6  1.0  1.0
+bond_coeff    2  30.0   1.6  1.0  1.0
+
+####################################
+####	THERMO AND INTEGRATION
+####################################
+thermo 1000000
+thermo_style   custom   step  temp  epair vol cpu
+timestep 0.01 
+
+####################################
+####    FIXES                #######
+####################################
+fix 1 all   nve
+fix 2 all  langevin   ${Temp} ${Temp} ${tdamp}  ${seedthermo}
+
+#Useful commands when running in parallel
+comm_style tiled
+fix bal all balance 10000 1.1 rcb
+comm_modify cutoff 3.0
+
+run ${run1}
+
+
+
+#########################################
+## WRITE RESTART AND ADDS TOPO II##
+#######################################
+#Where the restart (data) file after equilibration will be stored
+variable datafolder index Data
+shell mkdir ${datafolder}
+
+variable wname   index dataRestart.${simname}.
+variable newname index newdataRestart.${simname}.
+
+write_data ${wname}${readingtime}
+
+#Run the program that takes the restart file and places the topo II 
+shell ./Topo2_random_region ${readingtime} ${wname} ${newname} ${seedtopo}
+shell mv ${wname}${readingtime} ${datafolder}/${wname}${readingtime}
+
+
+
+
+
+
+
+
+
+
+##############################################################
+###  START RUN USING RESTART FILE WITH ADDED TOPO  ##
+##############################################################
+variable xyzname index XYZ_${simname}.xyz
+
+clear
+units lj
+atom_style angle 
+boundary        p p p
+neighbor 1.2 bin
+neigh_modify every 1 delay 1 check yes 
+
+restart 10000000 Data/Restart.topo2.
+
+variable rnewname index newdataRestart.${simname}.
+read_data ${rnewname}${readingtime}
+shell mv ${rnewname}${readingtime} Data/${rnewname}${readingtime}
+
+
+
+###############################
+####	BOX AND WALL	 ######
+###############################
+change_box all x final -101 101 y final -101 101 z final -101 101 boundary p p p  units box
+#fix WALL all wall/lj126 xhi EDGE 1.0 1.0 1.122462048 xlo EDGE 1.0 1.0 1.122462048 yhi EDGE 1.0 1.0 1.122462048 ylo EDGE 1.0 1.0 1.122462048 zhi EDGE 1.0 1.0 1.122462048 zlo EDGE 1.0 1.0 1.122462048 units box
+
+#######################################################
+####	PAIRS -- REPULSIVE + TOPO II 	#######
+#######################################################
+pair_style  hybrid lj/cut 1.12246 soft 1.12246
+pair_modify     shift yes
+pair_coeff      * * lj/cut 1.0 1.0 1.12246
+## NOW THERE IS TOPO2 -- TYPE 4 BEADS ARE SOFT AND CAN BE CROSSED
+pair_coeff      * 4 soft 2.0  1.12246
+pair_coeff      * 5 soft 20.0 1.12246
+
+
+####################################
+####	ANGLE	             #######
+####################################
+angle_style   cosine
+angle_coeff  1 5.0 #20 sigma for realistic DNA (1 bead = 2.5 nm)
+
+########################
+## PER PRIMI VICINI   ##
+########################
+bond_style fene
+#It turns off the LJ part of the FENE-bond potential between 1-2 atoms. However, the pairwise LJ interaction is still on
+special_bonds fene#<=== I M P O R T A N T (new command)
+bond_coeff   1 30.0   1.6  1.0  1.0
+bond_coeff   2 30.0   1.6  1.0  1.0
+
+####################################
+####	DUMPS	             #######
+####################################
+dump 2 all custom ${dumpfreq} ${folder}/${simname}.* id type x y z ix iy iz
+dump_modify 2 sort id
+
+##XYZ
+dump 4 all xyz ${dumptraj} ${xyzname}
+dump_modify 4 element O N Ca P Au
+
+####################################
+####	FIXES	             #######
+####################################
+timestep 0.01
+fix 1 all   nve  
+fix 2 all  langevin   ${Temp} ${Temp} ${tdamp}   ${seed00}
+
+#Useful commands when running in parallel
+comm_style tiled
+fix bal all balance 10000 1.1 rcb
+comm_modify cutoff 3.0
+
+thermo 10000
+thermo_style   custom step  temp  epair ebond eangle vol cpu
+run ${run2} #ONLY 5000x100'000 rather than 10'000x100'000
+################################################
+
+################
+## ULOOP    ####
+################
+clear
+
+variable folder     delete
+variable rname      delete
+variable xyzname    delete
+variable simname    delete
+variable jn         delete
+variable wname      delete
+variable rnewname   delete
+variable newname    delete
+variable seedthermo delete
+variable seedtopo   delete
+variable seed00     delete
+
+next jbn
+jump SELF #last line!!!
+
+### If e.g. I run this on 10 partitions of 1 processor,
+### and initialise the variable with 'uloop N'
+### it will run 10 simulations with 'jobnumber' taking 
+### values 1-10. Then when a particular simulation finishes, the 
+### script will be run again with the next value of jobnumber, 
+### until N simulations have been run.
+## SO ULOOP IS "SERIAL" BUT FOR SURE 10x1 PROCs ARE ALWAYS BUSY
diff --git a/1.Static/README.md b/1.Static/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..738535734376e1e510e0306b7832a57bc0ab1320
--- /dev/null
+++ b/1.Static/README.md
@@ -0,0 +1,17 @@
+### The bash.run.sh
+
+It contains:
+
+> 1.- The number of independent simulations to run. This is done by running the same lammps script (run.lam) with the same initial configuration (Eq.5_1.N1000.data) several times. The results from these simulations are stored into the folders REP1, REP2, ..., REPn.
+>
+> 2.- The instructions to produce the file *parameters.dat* which contains different random seeds that are used to produce independent simulations.
+
+### The run.lam script
+
+> 1.- The initial configuration contains a bead-and-spring polymer made by 1000 beads of type 1 that repeal each other via a purely repulsive LJ potential. Consecutive beads are connected via FENE bonds.
+>
+> 2.- The simulation is run for 3000000 timesteps. Then a restart file *dataRestart.Run.R1.0* is created.
+>
+> 3.- We use the program **Topo2_random_region.c++** to place the topo II  randomly along the DNA contour length. The arguments required by this programs are: timestep, input-file, output-file, random-seed. The input-file (*dataRestart.Run.R1.0*) is the restart file that comes from the previous equilibration. The output-file (*newdataRestart.Run.R1.0*) contains the position of the topo II represented by 50 beads of type 4 that interact through a soft potential, allowing strand crossing. In the static case the timestep is always 0, indicating that after the initial equilibration the topo II is placed. Finally, it is important to note that **the value of the variable Nbeads in the c++ must be set by hand to the total number of beads in the system, this is 1000**. 
+>
+> 4.- The output from the simulation is stored in the folder DUMPS
diff --git a/1.Static/bash.run.restart.sh b/1.Static/bash.run.restart.sh
new file mode 100644
index 0000000000000000000000000000000000000000..9f460c02c3edd61d87914df9839d2536e58964be
--- /dev/null
+++ b/1.Static/bash.run.restart.sh
@@ -0,0 +1,59 @@
+#!/bin/bash
+
+ncpu=64
+
+mf=`pwd`
+ff=$mf/MASTERFILES
+
+cd ${ff}
+c++ Topo2_random_region.c++ -o Topo2_random_region
+cd ${mf}
+
+
+
+for i in {1..64}
+do 
+  mkdir -p REP${i}
+  cd    REP${i}
+
+  cp ${ff}/run.lam.restart .
+  cp ${ff}/Topo2_random_region .
+  
+  ##Check the last restart file created in the previous run (example: Restart.topo2.100000000)
+  cd Data/
+  LastRFile=$(ls -tr|tail -1)
+  cd ../
+  #Obtain the timestep part of the name of the previous file (example: 100000000)
+  rtstep=$( echo "${LastRFile##*.}" )
+  echo ${rtstep}
+  #The DT parameter inside our lammps script 
+  Dt=1000
+  #Therefore the loop variable should start at:
+  lstart=$( echo $((rtstep / Dt)) )
+  
+  #Replace the line related to reading the restart file
+  sed -i "s/variable readingtime equal .*/variable readingtime equal ${rtstep}/g" run.lam.restart
+  
+  r1=$(od -An -N2 -i /dev/urandom)
+  r2=$(od -An -N2 -i /dev/urandom)
+  r3=$(od -An -N2 -i /dev/urandom)
+  r4=$(od -An -N2 -i /dev/urandom)
+  r5=$(od -An -N2 -i /dev/urandom)
+  echo "variable seed       equal ${r1}" >  parameters.dat
+  echo "variable seed00     equal ${r2}" >> parameters.dat
+  echo "variable seedin     equal ${r3}" >> parameters.dat
+  echo "variable seedtopo   equal ${r4}" >> parameters.dat
+  echo "variable seedthermo equal ${r5}" >> parameters.dat
+
+  nohup ~/lmp_mpi_29Oct2020 -in run.lam.restart < /dev/null > out &
+  
+  cd ../
+
+  vi=$(( ${i}%${ncpu} ))
+
+  if(( ${vi} == 0 )); then
+  wait 
+  fi
+done
+
+wait
diff --git a/1.Static/bash.run.sh b/1.Static/bash.run.sh
new file mode 100644
index 0000000000000000000000000000000000000000..2bc4123334fc95715fbba5732234eb0b85c30813
--- /dev/null
+++ b/1.Static/bash.run.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+ncpu=64
+
+mf=`pwd`
+ff=$mf/MASTERFILES
+
+cd ${ff}
+c++ Topo2_random_region.c++ -o Topo2_random_region
+cd ${mf}
+
+
+
+for i in {1..64}
+do 
+  mkdir REP${i}
+  cd    REP${i}
+
+  cp ${ff}/run.lam .
+  cp -r ${ff}/Init .
+  cp ${ff}/Topo2_random_region .
+  
+  r1=$(od -An -N2 -i /dev/urandom)
+  r2=$(od -An -N2 -i /dev/urandom)
+  r3=$(od -An -N2 -i /dev/urandom)
+  r4=$(od -An -N2 -i /dev/urandom)
+  r5=$(od -An -N2 -i /dev/urandom)
+  echo "variable seed       equal ${r1}" >  parameters.dat
+  echo "variable seed00     equal ${r2}" >> parameters.dat
+  echo "variable seedin     equal ${r3}" >> parameters.dat
+  echo "variable seedtopo   equal ${r4}" >> parameters.dat
+  echo "variable seedthermo equal ${r5}" >> parameters.dat
+
+  #nohup ~/lmp_mpi_29Oct2020 -in run.lam < /dev/null > out &
+  ~/SoftwareMD/lammps-29Oct20/exec/lmp_mpi_29Oct20 -in run.lam
+  
+  cd ../
+
+  vi=$(( ${i}%${ncpu} ))
+
+  if(( ${vi} == 0 )); then
+  wait 
+  fi
+done
+
+wait
diff --git a/README.md b/README.md
deleted file mode 100644
index 2da682af90b4ce6cd48fe8c693629388a9bb8792..0000000000000000000000000000000000000000
--- a/README.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# LAMMPS implementation of TopoII using and external code
-
-We model a torsionally relaxed (nicked) DNA plasmid 7.2 kbp-long as a bead-spring polymer made of 1000 beads with bead-size σ=2.5 nm=7.3 bp and connected by finitely extensible springs. The persistence length of the polymer is set to lp = 50 nm. Beads interact via a purely
-steric Lennard-Jones repulsion while the TopoII-bound segment is modelled as a 50 beads (L=360 bp)-long segment displaying soft interactions with the other beads thereby allowing the TopoII-bound segment to undergo strand-crossing with a small energy penalty (2 k<sub>B</sub>T). For details in the model and the system used we refer the reader to our paper: *D. Michieletto, et al.* "**Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation**".
-
-All the simulation scripts in this repository are set to start from a N=1000 beads thermally equilibrated polymer tied in a 5<sub>1</sub> torus knot. This and other initial configurations are provided inside the folder **0.InitialConfigurations**. The files are written in the correct format to be read by LAMMPS.
-
-The position of the TopoII-bound segment can be either: 
-
-* **1.Static**: Meaning that at the begining of the simulation (t=0), the position of the topoII is chosen randomly and then it stays in the same position during the course of the simulation.
-* **2.Random Jump**: The positions of the topoII is updated with a certain frequency and it is placed randomly along the contour length of the polymer.
-* **3. Jump to maximum density**: The positions of the topoII is updated with a certain frequency and it is placed in the site of maximum density of beads along the contour length of the polymer.
-
-A brief explanation of the implementation in each of these cases and the scripts to run these simulations are provided inside the corresponding folders in this repository.
-
-All the LAMMPS scripts have been tested using the current stable-version of LAMMPS (29-October-2020). To built the LAMMPS executables please make sure that the MOLECULE and USER-MISC packages are installed. These are standard packages that come with LAMMPS, and can be enabled before compiling, e.g. with the command: make yes-molecule.
-
-
-
-