Add overall README and fix typos

README

+# LAMMPS tutorials for beginners
+
+Here are three tutorials on LAMMPS, mostly geared towards students who would
+like to start using this software for simulating DNA/chromatin dynamics. The
+topics covered in the tutorials are as follows:
+
+- Tutorial 0 (tut0_lj_fluid)    - simulating a Lennard-Jones fluid
+
+- Tutorial 1 (tut1_polymer)     - simulating a homopolymer chain
+
+- Tutorial 2 (tut2_dna_protein) - simulating DNA-protein interactions
+
+I would recommend working through these tutorials in chronological order, as
+they get more complex from one to the next (e.g., more potentials used, more
+LAMMPS commands introduced).
+
+Within each tutorial folder, there is a bash script (init.sh). Running this
+script generates all the necessary files for running LAMMPS. For tutorials
+which ask you to play around with the parameter values for the potentials, you
+can change them within the bash script and then re-run it to generate new input
+files/run scripts for LAMMPS.
+
+If you are unsure at any point in these tutorial exercises, please consult
+the online LAMMPS documentation:
+
+   docs.lammps.org/Manual.html
+

tut0_lj_fluid/README

-# Tutorial 0 -- Lennard-Jones fluids
+# Tutorial 0 -- simulatin a Lennard-Jones fluid
 
 In this first tutorial, we use LAMMPS to perform molecular dynamics (MD)
-simulations of a Lennard-Jones (LJ) fluid (colloidal particles in a sovlent).
+simulations of a Lennard-Jones (LJ) fluid (colloidal particles in a solvent).
 In the simulation we have two types of particles (atoms) situated in a
 periodic box, and they interact with each other via a truncated and shifted LJ
 potential, which is given by
@@ -38,10 +38,10 @@ particle due to collisions with the solvent particles. eta(t) is a random
    <eta(t)> = 0
    <eta_i(t)eta_j(t')> = delta(t-t')delta_ij
 
-where the first delta in the second equation is a dirac delta and the second
+where the first delta in the second equation is a Dirac delta and the second
 one is a Kronecker delta, and i,j are indices running over Cartesian
 components. This type of equations is known as Langevin equations, and you
-will learn more about them in the Year 4 Statstical Physics course. Often MD
+will learn more about them in the Year 4 Statistical Physics course. Often MD
 simulations using this scheme are referred as 'Brownian/Langevin dynamics'
 simulations.
 
@@ -54,7 +54,7 @@ the online LAMMPS documentation:
 
 What to do:
 
-0. Familarise yourself with the LJ potential
+0. Familiarise yourself with the LJ potential
 
    Using your favourite plotting package, plot the truncated and shifted LJ
    potential for different parameter values (epsilon and rc) and have a think
@@ -88,7 +88,7 @@ What to do:
    b. Run the simulation
 
       You can use the pre-compiled version of LAMMPS available on the school
-      linux computers. Alternatively, you can also compile LAMMPS on your
+      Linux computers. Alternatively, you can also compile LAMMPS on your
       own computer (visit docs.lammps.org/Install.html for more info on how to
       install LAMMPS). To start the simulation, we use the command
 

tut1_polymer/README

@@ -33,12 +33,12 @@ polymer models is also known as a Kratky-Porod model.
 
 What to do:
 
-0. Familarise yourself with the bond and angle potentials
+0. Familiarise yourself with the bond and angle potentials
 
    Using your favourite plotting package, plot both the FENE and cosine
    potentials. Make sure you are happy with how these potentials do what they
    are meant to do in the simulations! Explore different parameter values and
-   see how that changes the shape of the potential as well as th structural
+   see how that changes the shape of the potential as well as the structural
    and dynamical properties of the system.
 
 1. Run the simulation with the default parameters