BioExcel, the leading European Centre of Excellence for computational biomolecular research, aims to support Life Science academic and industrial researchers in the effective use of HPC biomolecular software and continues BioExcel’s webinar series with its top experts in biomolecular modelling and simulations tools. Welcome!
Webinar #74: Temperature and pressure control using first-order stochastic algorithms
|Date:||November 14th, 2023|
|Time:||15:00 CEST (Central European Summer Time) UTC/GMT + 2h|
|16:00 EEST (Eastern European Summer Time) UTC/GMT + 3 h|
|Please do not forget to take into consideration the different time zones of joining the webinar!|
|Tool:||ZOOM (install the latest Zoom application before the webinar via https://zoom.us/download)|
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  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.
 Bussi, Donadio, and Parrinello, J. Chem. Phys. 126, 014101 (2007)
 Bernetti and Bussi, J. Chem. Phys. 153, 114107 (2020)
 Del Tatto, Raiteri, Bernetti, and Bussi, Appl. Sci. 12, 1139 (2022)
Giovianni Bussi - International School for Advanced Studies (SISSA)
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14.11.2023 15:00 +01:00 CET
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