期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 14, 期 12, 页码 6175-6182出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.8b00835
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资金
- Deutsche Forschungsgemeinschaft [Sto 247/11]
- bwUniCluster computing initiative of the State of Baden-Wurttemberg
- bwForCluster computing initiative of the State of Baden-Wurttemberg
As standard unbiased molecular dynamics (MD) simulations become impractical for sampling rare events, targeted MD employs a moving distance constraint to enforce rare transitions along some reaction coordinate x. To calculate free energy profiles from these nonequilibrium simulations via Delta G(x) = W(x) - W-diss(x), apart from the (readily obtained) work W(x) performed on the system, the dissipated work W-diss(x) is also required. By employing a second-order cumulant expansion of Jarzynski's equality combined with an analysis within Langevin theory, the dissipated work can be expressed via a nonequilibrium friction coefficient Gamma(NEQ)(x) that may be calculated on-the-fly from constraint force fluctuations. Adopting the ion dissociation of NaCl in water as a test system, this friction correction is shown to result in accurate free energy profiles, even for a modest number of simulations and at high constraint velocities. As a bonus, the analysis of Gamma(NEQ)(x) may yield valuable insight into the microscopic mechanism of friction.
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