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ThermostatsTable of contents
See GROMACS manual, Chapter 3, for details on how temperature coupling is applied and the types currently available.
General InformationThermostats are designed to help a simulation sample from the correct ensemble (i.e. NVT or NPT) by modulating the temperature of the system in some fashion. First, we need to establish what we mean by temperature. In simulations, the "instantaneous (kinetic) temperature" is usually computed from the kinetic energy of the system using the equipartition theorem. In other words, the temperature is computed from the system's total kinetic energy. So, what's the goal of a thermostat? Actually, it turns out the goal is not to keep the temperature constant, as that would mean fixing the total kinetic energy, which would be silly and not the aim of NVT or NPT. Rather, it's to ensure that the average temperature of a system be correct. To see why this is the case, imagine a glass of water sitting in a room. Suppose you can look very closely at a few molecules in some small region of the glass, and measure their kinetic energies. You would not expect the kinetic energy of this small number of particles to remain precisely constant; rather, you'd expect fluctuations in the kinetic energy due to the small number of particles. As you average over larger and larger numbers of particles, the fluctuations in the average get smaller and smaller, so finally by the time you look at the whole glass, you say it has "constant temperature". Molecular dynamics simulations are often fairly small compared to a glass of water, so we have bigger fluctuations. So it's really more appropriate here to think of the role of a thermostat as ensuring that we have (a) the correct average temperature, and (b) fluctuations of the correct size.
What Not To DoSome hints on practices that generally not a good idea to use:
What To DoSome hints on practices that generally are a good idea:
References
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