final changes commit

1_DNAModels/3_oxDNA/oxDNA1/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"
@@ -14,9 +17,6 @@ intl="initial_configuration_N${nbp}_phi0.6"
 
 #Number of cpu's to use in the simulation
 ncpu=1
-
-#Current working directory variable 
-cwd=`pwd`
   
   mkdir -p REP1
   cd    REP1
@@ -30,4 +30,4 @@ 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

1_DNAModels/3_oxDNA/oxDNA2/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"
@@ -14,9 +17,6 @@ intl="initial_configuration_N${nbp}_phi0.6"
 
 #Number of cpu's to use in the simulation
 ncpu=1
-
-#Current working directory variable 
-cwd=`pwd`
   
   mkdir -p REP1
   cd    REP1
@@ -30,4 +30,4 @@ 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

2_Melting/1_linear/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"
@@ -14,9 +17,6 @@ intl="linear.N${nbp}.lammps"
 
 #Number of cpu's to use in the simulation
 ncpu=1
-
-#Current working directory variable 
-cwd=`pwd`
   
   mkdir -p REP1
   cd    REP1
@@ -30,4 +30,4 @@ 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

README.md

@@ -10,7 +10,11 @@ Furtheremore, we will discuss how to:
 4. Analyse the output from simulations.
 
 ## Requirements
-In this section you will find the software neccessary for this tutorial and instructions on how to install it.
+In this section you will find the software neccessary for this tutorial and instructions on how to install it. The tutorial assumes that a LAMMPS executable  called **lmp\_mpi\_29Sep2021** exist into this folder (see below for installation).
+
+Also, we recomend to create an alias for ovito. To this end, open a terminal into your home directory and type *vim bash.rc*. Then add the line:
+
+alias=ovito
 
 ### Git
 Git is a distributed version control software. This is, a way to save changes over time without overwriting previous versions. The instructions to install it in *Windows, Linux and Mac* can be found in the following [Link](https://github.com/git-guides/install-git).
@@ -23,7 +27,7 @@ In this tutorial we will implement simulations of DNA using [oxDNA](https://dna.
 
 One important feature of the oxDNA model is that [recently](https://link.springer.com/article/10.1140/epje/i2018-11669-8) it was implemented as a package that can be build into LAMMPS. Here, I mentioned the general steps on how to build LAMMPS with this package (assuming that you are using a computer with either macOS or linux-OS such as Ubuntu). For different operating systems please follow instructions [here](https://docs.lammps.org/Install.html).
 
-We will work with the current stable release of LAMMPS (**29-September-2021**) that can be installed in the following way: Assuming that you have a terminal located in the **home** directory, you have to type:
+We will work with the current stable release of LAMMPS (**29-Sept-2021**) that can be installed in the following way: Assuming that you have a terminal located in the **home** directory, you have to type:
 
 > git clone -b stable https://github.com/lammps/lammps.git mylammps
 > 
@@ -33,13 +37,13 @@ We will work with the current stable release of LAMMPS (**29-September-2021**) t
 > 
 > cd ../
 > 
-> make yes-molecule yes-asphere yes-CG-DNA
+> make yes-molecule yes-asphere yes-CG-DNA yes-extra-molecule
 > 
-> make serial
+> make mpi
 > 
-> mv lmp\_serial ~/lmp\_serial_29Sep2021
+> mv lmp\_mpi ~/lmp\_mpi_29Sep2021
 
-With this, an executable with the name **lmp\_serial\_29Sep2021** shoul have been created in your home directory (*~/*).
+With this, an executable with the name **lmp\_mpi\_29Sep2021** shoul have been created in your home directory (*~/*). Copy the executable into this folder, where you downloaded the tutorial.
 
 ### Ovito
 In the tutorial we will learn how to visualize the output generated from simulations. To this end, we will use [Ovito](https://www.ovito.org) a visualization tool that can deal with aspherical particles. This is necessary to capture the planarity of bases in a nucleotide.