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cchiang2
lammps_tutorial
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# 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
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# Tutorial 0 -- Lennard-Jones fluid
s
# 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 so
v
lent).
simulations of a Lennard-Jones (LJ) fluid (colloidal particles in a sol
v
ent).
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
d
irac delta and the second
where the first delta in the second equation is a
D
irac 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 Stat
i
stical Physics course. Often MD
simulations using this scheme are referred as 'Brownian/Langevin dynamics'
simulations.
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@@ -54,7 +54,7 @@ the online LAMMPS documentation:
What to do:
0. Familarise yourself with the LJ potential
0. Famil
i
arise 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
...
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@@ -88,7 +88,7 @@ What to do:
b. Run the simulation
You can use the pre-compiled version of LAMMPS available on the school
l
inux computers. Alternatively, you can also compile LAMMPS on your
L
inux 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
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@@ -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. Famil
i
arise 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 th
e
structural
and dynamical properties of the system.
1. Run the simulation with the default parameters
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