(Note: These tutorials are meant to provide
illustrative examples of how to use the AMBER software suite to carry out
simulations that can be run on a simple workstation in a reasonable period of
time. They do not necessarily provide the optimal choice of parameters or
methods for the particular application area.)
Copyright Ross Walker 2004
TUTORIAL 1
Simulating a DNA polyA-polyT Decamer
By Ross Walker
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| Pictured above is the average structure from a 1 nanosecond molecular dynamics simulation of a 10 base pair poly(A)-polt(T) DNA duples. The calculation was run in explicit solvent using periodic boundaries and the particle mesh Ewald method of treating long range electrostatics. The average structure was generated using ptraj by RMS fitting all of the DNA atoms in 1,000 snapshots at 1 ps intervals and then averaging the coordinates. |
1) Introduction
The purpose of this tutorial is to provide an initial introduction to setting up and running simulations using the AMBER software. In this tutorial we run a series of simulations on a poly(A)-poly(T) decamer of DNA. We will first figure out how to generate a starting structure and then use this structure to construct the necessary input files for running sander, the main molecular dynamics engine supplied with AMBER.
In order to run a classical molecular dynamics simulation with Sander a number of files are required. These are (using their default filenames):
prmtop - a file containing a description of the molecular topology and the necessary force field parameters.
inpcrd (or a restrt from a previous run) - a file containing a description of the atom coordinates and optionally velocities and current periodic box dimensions.
mdin - the sander input file consisting of a series of namelists and control variables that determine the options and type of simulation to be run.
In the first section of this tutorial we shall use the tools provided with AMBER to create prmtop and inpcrd files for both in vacuo and solvated systems. We will then run sander to perform minimisation followed by molecular dynamics and eventually get to the point where we can reproduce the picture shown above.
Since running these simulations using explicit solvent can be expensive, we will also use some models that include solvent effects implicitly.
The approximate order of this tutorial will be as follows:
Create the prmtop and inpcrd files: This is a description of
how to generate the initial structure and set up the molecular
topology/parameter and coordinate files necessary for performing
minimisation or dynamics with sander.
An introduction to minimisation and molecular dynamics. Run
short MD simulations in-vacuo. Perform basic analysis such as
calculating root-mean-squared deviations (RMSd) and plotting various energy
terms as a function of time. Visualising results with VMD.
Minimisation and molecular dynamics in implicit solvent:
Setting up and running equilibration and production minimisation and
molecular dynamics simulations for our DNA model using the Born implicit
solvent model.
Minimisation and molecular dynamics in explicit solvent: Setting up and running equilibration and production simulations for our DNA model using TIP3P explicit water.
Throughout this tutorial filenames and command line switches will be written in courier or an equivalent monospace font while program names such as sander will be written in the same font but italicised. Input files will be coloured in red and output files in green.
(Note: These tutorials are meant to provide
illustrative examples of how to use the AMBER software suite to carry out
simulations that can be run on a simple workstation in a reasonable period of
time. They do not necessarily provide the optimal choice of parameters or
methods for the particular application area.)
Copyright Ross Walker 2004
