All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method.
All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method.
复制标题
使用滑块迭代对角化方法对细菌视紫红质的正常模式进行全原子计算。
DOI：
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发表时间：
2006
影响因子：
5.5
通讯作者：
J. Bowman
中科院分区：
文献类型：
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作者：
A. Kaledin;Martina Kaledin;J. Bowman
分子振动的常规简正模分析需要计算和存储 Hessian 矩阵。对于典型的生物系统来说，这样的存储可以达到几千兆字节，这给直接实施带来了困难。在这项工作中，我们讨论了一种迭代块方法来执行 Hessian 矩阵的完全对角化，同时仅在内存中存储一些向量。迭代方法基于戴维森算法的共轭梯度公式，用于同时优化 L 个根，在我们的例子中为 10 < L < 300。通过自动将新向量添加到每个锁定（收敛）根的搜索空间中并保持新向量与先前确定的特征向量正交，进一步修改该过程。然后通过应用投影仪将较高的激发态与正交约束收敛到锁定的根，该投影仪使用每次迭代执行一次的读取倒回步骤来执行。这允许在不增加计算机内存的情况下收敛尽可能多的根。所需的 Hessian 向量乘积按如下方式即时计算：Kp = dgp/dt，其中 K 是质量加权 Hessian 矩阵，gp 是沿 p 的梯度。该方法已被应用到 TINKER 分子设计代码套件中。初步结果显示了细菌视紫红质 (bR) 正常模式高达 300 cm(-)(1) 以及 2840 至 3680 cm(-)(1) 之间的高频范围。有证据表明，在 ∼1.4 cm(-)(1) 处存在高度局部化的非集体模式，这是由 bR 的细胞质和细胞外结构域之间的长程相互作用引起的。
Conventional normal-mode analysis of molecular vibrations requires computation and storage of the Hessian matrix. For a typical biological system such storage can reach several gigabytes posing difficulties for straightforward implementation. In this work we discuss an iterative block method to carry out full diagonalization of the Hessian while only storing a few vectors in memory. The iterative approach is based on the conjugate gradient formulation of the Davidson algorithm for simultaneous optimization of L roots, where in our case 10 < L < 300. The procedure is modified further by automatically adding a new vector into the search space for each locked (converged) root and keeping the new vector orthogonal to the eigenvectors previously determined. The higher excited states are then converged with the orthonormality constraint to the locked roots by applying a projector which is carried out using a read-rewind step done once per iteration. This allows for convergence of as many roots as desired without increasing the computer memory. The required Hessian-vector products are calculated on the fly as follows, Kp = dgp/dt, where K is the mass weighted Hessian, and gp is the gradient along p. The method has been implemented into the TINKER suite of molecular design codes. Preliminary results are presented for the normal modes of bacteriorhodopsin (bR) up to 300 cm(-)(1) and for the high frequency range between 2840 and 3680 cm(-)(1). There is evidence of a highly localized, noncollective mode at ∼1.4 cm(-)(1), caused by long-range interactions acting between the cytoplasmic and extracellular domains of bR.