Molecular dynamics simulations for biological systems: Setup

Setup instructions

To participate in this workshop, you will need the software described below. In addition, you will need an up-to-date web browser.

There will be NO time allocated to do this during the workshop, please install it beforehand.

SSH client

Windows

Install MobaXterm from http://mobaxterm.mobatek.net. You will want to get the Home edition (Installer edition).

macOS

Although macOS comes with SSH pre-installed, you will likely want to install XQuartz to enable graphical support. Note that you must restart your computer to complete the installation.

Linux

Linux users do not need to install anything, you should be set!

Visualisation tools:

Pymol

Install Pymol from SourceForge or pymol.org.

VMD

Install VMD

Schedule

Setup Download files required for the lesson
00:00 1. Overview of AmberTools20 What is the AmberTools package?
00:05 2. Environment set up and downloading files Which software will be used in this workshop?
00:10 3. Preparing your PDB file What should I check before preparing a simulation?
00:25 4. Parameterising your ligands How do I generate parameters for non-conventional residues?
00:40 5. System set up How do I create topology and coordinate files?
00:50 6. Energy minimisation What should I do after generating my system’s topology and coordinates?
How do I refine and remove bad contacts from the initial structure?
01:00 7. Thermalisation and Pressure Equilibration How do I equilibrate my system with sander?
01:20 8. Production runs How long should I run my production runs?
01:30 9. Basic analysis of the trajectories Has my simulation converged?
Is my protein stable?
01:40 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.