Pracht Philipp, Grimme Stefan, Bannwarth Christoph, Bohle Fabian, Ehlert Sebastian, Feldmann Gereon, Gorges Johannes, Müller Marcel, Neudecker Tim, Plett Christoph, Spicher Sebastian, Steinbach Pit, Wesołowski Patryk A, Zeller Felix
Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
J Chem Phys. 2024 Mar 21;160(11). doi: 10.1063/5.0197592.
Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.
构象异构体-旋转异构体采样工具（CREST）是一个用于高效、自动探索分子化学空间的开源程序。它最初由普拉赫特等人[《物理化学化学物理》22, 7169 (2020)]开发，作为扩展紧束缚水平（xTB）计算的自动驱动程序，提供了多种分子动力学和元动力学模拟、几何优化以及分子结构分析功能。所实现的算法包括构象采样的自动化程序、明确溶剂化研究、绝对分子熵的计算以及分子质子化和去质子化位点的识别。计算设置为并行运行，提供高效的单节点并行化。CREST旨在要求用户输入最少，并附带GFNn-xTB哈密顿量和GFN-FF力场的实现。此外，可以轻松创建与任何量子化学和力场软件的接口。在本文中，我们展示了CREST代码的最新进展，并展示了该程序最重要功能的一系列应用。一个重要的新特性是重构的计算后端，它显著加快了中小尺寸药物分子的采样速度，并允许进行更复杂的设置，例如量子力学/分子力学和最小能量交叉点计算。
