Paper title:

Thermostat algorithms for molecular dynamics simulations

 

Journal:

Adv. Polym. Sci. (2005) 173:105?149

 

Author/s:

Philippe H. H?nenberger

Laboratorium f?r Physikalische Chemie, ETH Z?rich, CH-8093 Z?rich, Switzerland

 

Summary:

This is a 45-page document that explains in detail the principles of using a thermostat in molecular dynamics (MD) simulations.

Firstly, the paper discusses about ensembles. Then it moved to the discussion about how to modify the basic Newtonian equations of motion in order to account for the changes in velocities brought about by “thermostatting”. Afterwards, it reviews the various thermostat algorithms available by describing their principles, advantages, and limitations.

A thermostat algorithm is used to maintain a constant “average” temperature during MD simulations. Because temperature is directly related to atomic kinetic energy and hence, to atomic internal velocities, maintaining temperature constant (or slightly fluctuating around an average) necessitates the control of the rate of change of these velocities. Therefore, a thermostat algorithm modifies the basic Newtonian equation in order to generate a thermodynamical ensemble having a constant temperature.

A thermostat works by first defining an instantaneous temperature (usually, temperature at experimental conditions to mimic real conditions). This will then be matched to the reference temperature of the heat bath to which the system would be coupled.

Contribution and application:

In real-life RO desalination processes, temperature is constant. Hence, it is important, especially on a molecular level, to maintain temperature as constant as possible, with the least fluctuations. In this document, I focused on learning about the basics of thermostats and ensembles so that I can choose which thermostat I should use to keep my simulation system under a constant temperature.

By: Hannah Ebro

hannah@gist.ac.kr