Abalone in education

Abalone is designed in a such way that typical tasks are performed exclusively through a graphical interface. In each method, in most cases, you can rely on the default settings. Moreover, the molecule drawn by the mouse already has the parameters of the force field (ad hoc mode). Therefore, when starting a new task, you can quickly get a simple, but already working model. Then, step by step, this model can be modified by replacing the default parameters.

Although the program is oriented for biopolymers, it has default parameters for all elements, which makes it suitable for demonstrating a wide variety of chemistry topics. We offer some demonstrations:

• Wetting of the hydrophilic and hydrophobic surfaces
• Water ice in nanotubes
• Protein folding
• DNA-ligand interactions

An in-depth study of the methods of molecular mechanics can be facilitated by a set of various algorithms. Default algorithms work well for most tasks, but often the best solution is to use alternative algorithms. For example:

• Although molecular dynamics is the universal and most popular method of simulation, nevertheless thermodynamic properties are better simulated using one of the Hybrid Monte Carlo variants. We recommend xHMC.
• For optimization, especially for large models, conjugate gradients are the method of choice. However, in some cases, we do not need to do a complete local optimization. For example, it is desirable to eliminate the hard hits of several atoms, but maintain a common conformation or preserve symmetry. In this case, it is better to do several steps by the steepest descent method.
• By default, a very efficient Bussi-Donadio-Parrinello method is used for thermostating. However, if the model is very far from equilibrium, for example, this is a preliminary made by hands model, equilibrium can be achieved very long. In this case, the Lowe method is good.
• When simulating a protein without explicit water, the Generalized Born method is used. However, in those problems where we agree to a more crude method, and speed is important to us, we can use the fast Sheffield method.

Articles about how Abalone can be used in training courses:

Benjamin Spitznagel, Paige R. Pritchett, Troy C. Messina, Mark Goadrich, Juan Rodriguez 2016 An undergraduate laboratory activity on molecular dynamics simulations. Biochemistry and Molecular Biology Education 44(2):130–139 DOI 10.1002/bmb.20939

Donald E. Elmore 2016 Why Should Biochemistry Students Be Introduced to Molecular Dynamics Simulations—And How Can We Introduce Them? Biochemistry and Molecular Biology Education 44(2):118-123 DOI 10.1002/bmb.20943