(1b) Advanced Sampling Using Ssages: Basics, Practical Tips and More

Advanced sampling techniques, in particular ones which can compute free energies and reactive pathways, are an important new development in molecular simulations. Stretching back 20 years to their origins in multicanonical sampling and the first “flat histogram” methods, significant improvements have been made that make the calculation of complex free energy landscapes possible. Indeed, these techniques have been applied to many disparate problems, such as material constant calculations, determination of native protein folding states and pathways, equilibrium phase diagrams, and self-assembling materials.

In this short course, we will explain the theoretical underpinnings behind common sampling techniques, and discuss the relative merits of different techniques for a given problem. This will be facilitated through demonstrations using our powerful sampling suite SSAGES [1] (pronounced “sages”). SSAGES encompasses a variety of advanced sampling techniques for determining free energy landscapes and reactive pathways. Specifically, we will discuss the application of SSAGES to obtain elastic properties, polymer conformational energies, and nanoparticle potentials of mean force. We will walk through the definition of collective variables necessary for advanced sampling, discuss what makes a good collective variable, and how to address common issues encountered in the convergence of advanced sampling methods. We will also perform hands-on examples to give participants a feel for how SSAGES works, and how to understand advanced sampling methods in general.

1. Sidky, Hythem, Yamil J. Colón, Julian Helfferich, Benjamin J. Sikora, Cody Bezik, Weiwei Chu, Federico Giberti et al. "SSAGES: Software Suite for Advanced General Ensemble Simulations." The Journal of chemical physics 148, no. 4 (2018): 044104.