Conte Riccardo, Gandolfi Michele, Moscato Davide, Aieta Chiara, Valtolina Stefano, Ceotto Michele
Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy.
Dipartimento di Informatica "Giovanni Degli Antoni", Università degli Studi di Milano, Milano, Italy.
J Comput Chem. 2025 May 5;46(12):e70118. doi: 10.1002/jcc.70118.
Vibrational spectroscopy calculations based on classical molecular dynamics simulations are widely employed in a variety of popular fields, for instance, computational biochemistry and materials science. These calculations commonly rely on the Fourier transform of the velocity autocorrelation function. One major drawback of the method is that calculated spectra are difficult to interpret due to the large number of closely spaced signals. In this paper, we show how theory can help to overcome this issue by means of a time-average technique, and we introduce free software to perform such calculations for anyone who may take advantage of it. The studies presented here involve the classical vibrational spectra of aniline microsolvated by a water molecule and gas-phase deoxyguanosine. The software is made available in the form of a free web-platform, named SEMISOFT (http://semisoft.unimi.it/), whereby, upon upload of the classical trajectory, the user gets the corresponding time-averaged spectrum. Furthermore, since the evaluation of response functions through autocorrelated data is quite a general approach, the web-platform can be directly employed in many other research fields besides chemistry.
基于经典分子动力学模拟的振动光谱计算在各种热门领域中被广泛应用，例如计算生物化学和材料科学。这些计算通常依赖于速度自相关函数的傅里叶变换。该方法的一个主要缺点是，由于大量紧密间隔的信号，计算出的光谱难以解释。在本文中，我们展示了理论如何通过时间平均技术帮助克服这个问题，并且我们介绍了一款免费软件，供任何可能从中受益的人进行此类计算。这里展示的研究涉及由一个水分子微溶剂化的苯胺以及气相脱氧鸟苷的经典振动光谱。该软件以名为SEMISOFT（http://semisoft.unimi.it/）的免费网络平台形式提供，通过上传经典轨迹，用户可以获得相应的时间平均光谱。此外，由于通过自相关数据评估响应函数是一种相当通用的方法，该网络平台除了化学领域外，还可直接应用于许多其他研究领域。
