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Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach

机译:平均力计算的潜力:多步自适应偏置力方法

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The adaptive biasing force (ABF) scheme is a powerful molecular-dynamics based method for overcoming barriers of the free-energy landscape. Integration of the mean force measured along a chosen reaction coordinate (RC) yields the so-called potential of mean force (PMF). The RC is a coarse-grained description of the transition mechanism. The mean force is estimated by accruing and averaging the instantaneous force exerted on the system. The PMF is then used to bias the standard dynamics of the system in order to improve sampling in the RC. We show that faster exploration of the reaction pathway can be achieved by running multiple walkers in parallel and exchanging information affixed intervals in the course of the simulation. Numerical experiments performed on the prototypical deca-alanine peptide demonstrate that the convergence properties of the free-energy calculation are globally improved through a more efficient exploration of compact configurations reflected in parallel valleys of the free-energy landscape. Diffusion along the RC is further enhanced by a selection mechanism, whereby far-reaching walkers are cloned, replacing less effective ones.
机译:自适应偏置力(ABF)方案是一种强大的基于分子动力学的方法,可以克服自由能格局的障碍。沿所选反作用坐标(RC)测得的平均力的积分产生了所谓的平均力电位(PMF)。 RC是对过渡机制的粗粒度描述。平均力是通过累加和平均施加在系统上的瞬时力来估算的。然后使用PMF偏置系统的标准动态,以改善RC中的采样。我们表明,通过在模拟过程中并行运行多个walker并交换信息附加的间隔,可以更快地探索反应路径。在原型十丙氨酸肽上进行的数值实验表明,通过更有效地探索在自由能景观平行谷中反映的紧凑构型,可以全面提高自由能计算的收敛性。通过选择机制进一步增强了沿RC的扩散,从而克隆了影响深远的步行者,从而取代了效率较低的步行者。

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