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16544385784
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note
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In thermodynamics, the term isothermal usually means that the temperature of the system remains constant during the process. Here we use the term to mean that the system is in contact with a bath at constant temperature, though the temperature of the system is not necessarily constant during the process. In fact, the system's temperature is not even defined when we deal with nonequilibrium processes. The same applies to the term isobaric.
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There is a third type of method, such as the isokinetic Gaussian thermostat, in which equations of motion are modified by the addition of deterministic terms, but without introducing new degrees of freedom. The nonequilibrium work relation has been established for the isokinetic Gaussian thermostat. See, D. J. Evans, Mol. Phys. 101, 1551 (2003).
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note
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Recall that the Gaussian nature of the work distribution depends on the assumption of the overdamped Langevin equation (Sec. III D). It is desirable to test this assumption in simulations.
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52
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16544394469
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note
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One way of doing this is the Langevin piston method, which is introduced in Sec. II G.
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