A tutorial for molecular dynamics simulations using Amber package

Abstract

In this paper we present a tutorial for performing molecular dynamics calculations utilizing Amber package. Through it we explain the function of each step in a theoretical work of MD, thus enabling the application of acquired knowledge to other systems without many difficulties. For this tutorial, we simulated by MD and analyzed various geometrical and structual parameters for doxycycline, a potent antimicrobial agent.

Keywords

• doxycycline
• qm/mm
• educational
• cluster