Simulating DNA with Different Solvation Models¶
Overview¶
The purpose of this tutorial is to provide an introduction to setting up and running simulations using the AMBER software, and to explore the effect of solvation conditions and cut offs on DNA structures observed in molecular dynamics simulations. It is based on AMBER 23 and AmberTools 23 but should be used with the most recent version of Amber available. In this tutorial we run a series of simulations on the Dickerson dodecamer, a well known DNA structure. 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 molecular dynamics engine supplied with AmberTools.
In this tutorial, you will simulate a short DNA duplex in different solvent conditions. Because DNA is a highly charged molecule, the solvation environment is very important.
You will perform four simulations of the DNA structure in different solvent conditions.:
DNA in vacuum with a short simulation cut-off.
DNA in vacuum with no simulation cut-off.
DNA in implicit solvent.
DNA in explicit solvent with ions.
Learning Outcomes¶
After completing this tutorial, you will be able to
Use tleap to prepare vacuum and solvated simulated systems.
Be able to explain the choice of periodic box shape (box vs. oct) when preparing solvated systems.
Run minimization, vacuum, implicit solvent, and explicit solvent simulations of DNA using sander.
Analyze energies. RMSD, and trajectory movies to assess simulations.
Create plots with xmgrace or Python.
Visualize simulation trajectories using VMD or Python and pytraj.
Explain the effect of solvent conditions and cut-off on simulation of DNA.