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Subsections



Adaptive Tempering

Adaptive tempering is akin to a single-copy replica exchange method for dynamically updating the simulation temperature. The temperature $ T$ is a new random variable in the range $ [Tmin,Tmax]$ that is governed by the equation $ dE/dT = E-E(T)-1/T+sqrt(2)T\xi$ , where $ \xi$ is Gaussian white noise. The effect is that when the potential energy for a given structure is lower than the (so far calculated) average energy, the temperature is lowered. Conversely when the current energy is higher than the average energy, the temperature is raised. The effect is faster conformational sampling to find minimum energy structures. The method is implemented exactly as described by Zhang and Ma in J. Chem. Phys. 132, 244101 (2010) (using Equation 18 of their paper to calculate the average energy at a given temperature from the histogram of energies).

The dynamic temperature is realized either by changing the temperature of the Langevin thermostat or by velocity rescaling.

NAMD parameters

The following parameters are used to adaptive tempering:


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