Molecular dynamics (MD) enables studying the dynamic behaviour of molecular systems at an atomic scale. The preparation of molecular dynamics simulations for biological systems can be difficult and tricky. Additionally, subtle changes in the setup process can often affect the accuracy and robustness of the results. This course aims to showcase a consistent protocol to set up your system in order to run MD simulations using AMBER.
This course covers basic tools and technologies needed to succeed in setting up a MD simulation with the AmberTools suite, and will be run with hands-on exercises. It provides a background to the preparation of biological systems for molecular modelling and offers practical experience in creating topologies successfully. You will learn about the intricacies behind the molecular modelling of biological systems, such as the practical skills required to handling and preparing PDB files.
At the end of this session you will be able to …
- Describe the main features of the AmberTools package
- Build topologies and coordinates ready to use in AMBER software
- Perform and analyse MD simulations
The duration of the sessions will be between 1 and 2 hours, depending on the level of interactivity.
Trainers:
- Carolina Estarellas (UB)
- Salome Llabres (UB)
Prerequisites
In this lesson we use AmberTools which will be already installed in the workstations. The following is expected:
- Comfortable using the Linux command line.
- Prior experience with MD or Biological systems knowledge are not required.