Overview of Amber Tutorials
If you are new to simulations, here are the general steps involved:
What types of ions/molecules do you have in your system?
Do you have a force field for each type of ion/molecule? If you don't how will you obtain or derive it?
Will you run your simlulation with explicit or implicit solvent? Which model for explicit solvent will you employ?
1. Building a System
This is the most complicated step. Before you start a simulation you will need to decide a number of items:
2. Relaxing the System
Once you have built the system, then you will want to get rid of bad contacts in the solute and if you have explicit solvent and/or ions, you will want to relax them around the solute to form a stable system.
3. Collecting Trajectories under Production Run Conditions
Amber has a number of production run MD engines including sander, sander.MPI, pmemd, pmemd.cuda, pmemd.cuda.MPI and others. For a full list and the differences please see the manual.
4. Analyzing Data
Once the trajectory is collected, you'll want to analyze the data. This is often the most time consuming part of a project and one that will need to be customized to your scientific question.
The Amber tutorials are organized with these items in mind in a modular fashion so that you can learn about each step as you need it.
General introductory case studies
Case studies have been developed that cover a lot of these steps collectively. Some of these tutorials are meant to provide illustrative examples of how to use the AMBER software suite. These 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. These should not be used as a standard for excellent science but rather a guide for using the software.
Please refer to published papers for better guidance regarding scientific methods and the Amber Reference Manual for implementation of specific flags.
Two of the most basic case studies are:
More Advanced Methods
For tutorials on more advanced methods, please see the specific area of the Amber Reference Manual and the correpsonding section of the Tutorials webpage (sections 6-9).