Bioexcel Webinar  #74 Temperature and pressure control using first-order stochastic algorithms
Channel: BioExcel CoE
Date: 2023-11-15

Molecular dynamics (MD) simulations are commonly conducted under constant temperature and/or pressure conditions to closely emulate experimental settings. The corresponding algorithms (i.e., thermostats and barostats) are hence designed to enable the transfer of thermal energy or of mechanical work from an external bath. Over the past decades, various algorithms have been proposed, extending Hamilton's equations through first or second-order, stochastic or deterministic approaches, or combining MD with Monte Carlo methods. In this presentation I will focus on first-order stochastic algorithms for temperature [1] and pressure [2,3] control. Specifically, I will show that these algorithms usually strike a good balance between the possibility of customizing relaxation properties and the ease of choosing control parameters. I will show how the formal connection with Monte Carlo allows to develop robust integrators for which violation of detailed balance can be numerically quantified during production simulations. Practical examples using the GROMACS code will be discussed.

[1] Bussi, Donadio, and Parrinello, J. Chem. Phys. 126, 014101 (2007)

[2] Bernetti and Bussi, J. Chem. Phys. 153, 114107 (2020)

[3] Del Tatto, Raiteri, Bernetti, and Bussi, Appl. Sci. 12, 1139 (2022)

Presenter 

Giovanni Bussi
International School for Advanced Studies (SISSA)

Biography: During my PhD, under the supervision of Prof. Elisa Molinari at the Università di Modena and Reggio Emilia, my research was focused on the ab initio computation of optical properties in low-dimensional systems. Afterwards, I joined the group of Prof. Michele Parrinello at ETH Zurich and started working in the field of computer simulation of molecular systems, with a special focus on rare events and biological problems. I then spent an additional year in Modena, working on the modeling of nonequilibrium experiments. Since September 2009 I have been working at SISSA as an assistant professor (tenured in 2014, full professor in 2020), where I have started a project on the simulation of nucleic acids. My research has been supported by an ERC starting grant (2012) and by a PRIN grant (2023). My research is mostly focused on (a) the study of RNA dynamics and (b) the development of the open source software PLUMED. In addition, I am interested in the development of fundamental algorithms for molecular dynamics, including thermostats and barostats.

X: @bussilab

LinkedIn: Giovanni Bussi