final changes commit

3_oxView/2_equilibration/bash.run.sh

 #!/bin/bash
+#Current working directory variable 
+cwd=`pwd`
 
 #Location of the LAMMPS executables
-LAMMPSparallel="/Disk/ds-sopa-personal/ygutier2/SoftwareMD/lammps-29Sep2021/exec/lmp_mpi_29Sep2021"
+LAMMPS="${cwd}/../../lmp_serial_29Sept2021"
+LAMMPSparallel="${cwd}/../../lmp_mpi_29Sept2021"
 
 #Name of the lammps script to run
 lscript="oxDNA.commands"
@@ -30,4 +33,4 @@ cwd=`pwd`
   echo "variable seed equal ${r1}"   >  parameters.dat
   echo "variable seed1  equal ${r2}" >> parameters.dat
   
-  mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
+  mpirun -np ${ncpu} ${LAMMPSparallel} -in ${lscript}
\ No newline at end of file