Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
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DOI：
10.1063/1.480139
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发表时间：
1999-11-01
影响因子：
4.4
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Bartels, C;Schaefer, M;Karplus, M
二维自适应伞采样的第一伞坐标等于系统的势能和第二伞坐标等于一个功能，区分重要的折叠构象从展开构象的平衡性质的复杂的生物系统被用来确定。与以势能为伞坐标的一维自适应伞采样（多规范采样）相比，在某些情况下可以得到更可靠的结果。该方法被施加到一个螺旋肽（RN 24）与分析连续溶剂的潜力结合的PARAM 19力场的CHARMM。这种有效势能函数已被证明可以描述溶剂化肽的结构偏好。采用二维方法，以偏离螺旋结构为第二伞坐标，得到了肽RN 24的结构性质和热力学性质的收敛描述。特别是，我们发现，RN 24的螺旋的形成发生的过渡伴随着一个特征峰的热容。描述了一种形式主义，使用加权直方图分析方法方程的自洽解决方案获得的加权因子，联合收割机从一系列具有不同偏差的模拟的结果，并计算作为温度的函数的任何动力学变量的系综平均值，而不需要从模拟中提取的态密度。它示出了如何的形式主义可以用来计算系统的热力学性质。(C)1999年美国物理学会。[S0021-9606（99）50340-1]。
Two-dimensional adaptive umbrella sampling with the first umbrella coordinate equal to the potential energy of the system and the second umbrella coordinate equal to a function that discriminates important folded conformations from unfolded conformations is used to determine the equilibrium properties of complex biological systems. Compared to one-dimensional adaptive umbrella sampling with the potential energy as umbrella coordinate (multicanonical sampling), more reliable results can be obtained in certain cases. The method is applied to a helical peptide (RN24) with an analytical continuum solvent potential in combination with the PARAM19 force field of CHARMM. This effective potential energy function has been shown to describe the structural preferences of solvated peptides. With the two-dimensional approach and the deviation from the helical structure as the second umbrella coordinate, a converged description of the structural properties and the thermodynamics of the peptide RN24 is obtained. In particular, we find that the formation of the helix of RN24 occurs as a transition accompanied by a characteristic peak in the heat capacity. A formalism is described that uses the weighting factors obtained from a self-consistent solution of the weighted histogram analysis method equations to combine the results from a series of simulations with different biases and calculate the ensemble average of any dynamical variable as a function of the temperature without the need for extracting the density of states from the simulations. It is shown how the formalism can be used to calculate thermodynamic properties of the system. (C) 1999 American Institute of Physics. [S0021-9606(99)50340-1].