无需粗粒化即可模拟粗粒化模拟：通过阻尼短程相互作用增强采样。

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

机构信息

Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

出版信息

J Chem Phys. 2010 Aug 28;133(8):084101. doi: 10.1063/1.3478526.

PMID:20815554

Abstract

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

摘要

提出了阻尼短程相互作用（DSRI）方法，通过在平滑势能表面上传播原子尺度系统来模拟粗粒化模拟。DSRI 方法具有典型粗粒化模拟提供的增强采样的优点，而无需进行粗粒化。我们的方法用于模拟液态水、丙氨酸二肽折叠和二肉豆蔻酰磷脂酰胆碱脂质的自组装。在每种情况下，我们的方法都显著加速了动力学，而没有显著改变自由能表面。讨论了 DSRI 模拟的附加见解以及将我们的 DSRI 方法与哈密顿复制交换分子动力学耦合的前景。