Interpolation for molecular dynamics simulations: from ions in gas phase to proteins in solution

Abstract

The interpolation technique has shown many promises for simulating chemical dynamics with quantum chemical accuracy at molecular mechanics speed. This is achieved by constructing analytic potential energy surfaces with quantum chemical information at multiple conformational points, without assuming any functional form for the potentials. Here, we briefly review the course the method was developed over the past few decades, with a special focus on the activities in Korea. We also describe its strengths and weaknesses toward describing condensed phase chemical dynamics with the present implementations. Perspectives for future developments toward increasing applicability are discussed as concluding remarks.

Effect of Underdamped Vibration on Excitation Energy Transfer: Direct Comparison between Two Different Partitioning Schemes

“…Namely, we can still properly account for the vibrational effects on EET by treating them completely classically. This aspect will indeed be beneficial when one has to adopt a complex potential model 82 where quantum mechanical treatments of vibrations are practically impossible. In addition, even a quantum treatment may have artifacts as exemplified by the lack the double phonon resonance and by the noticeably smaller height of the 174 cm −1 peak with VBM-(1,2).…”

Constructing an Interpolated Potential Energy Surface of a Large Molecule: A Case Study with Bacteriochlorophyll a Model in the Fenna–Matthews–Olson Complex

“…When the displacement is too excessive, the potential will subsequently be excessively low. 33 When there are an infinite number of data points, this issue will not be a problem as the weight of a data point at a large distance quickly decays to zero. However, in the practical application, if there is no data point at a shorter distance than the point with a negative Hessian character, it can become quite a serious issue.…”

“…For completeness, we will first briefly overview the technical aspects of the interpolation method. Curious readers can refer to historic developments ,,− of the technique and the related recent reviews. , Hereafter, for simplicity, we will use IM to refer either literally to interpolation mechanics or more loosely to the interpolation approach, unless such a use causes excessive ambiguity. For example, we will denote interpolated PES as IM PES and the interpolation region as IM region.…”

“…As the size of the conformational space becomes exponentially larger with the system’s dimensionality, efficiently selecting the data point locations will be important to render the PES interpolation a viable approach for a large system. Another issue that is frequently encountered during the interpolated PES construction is the creation of unphysically low energy traps by data points with negative Hessian characters. , Because such traps tend to lock the interpolated molecule in regions of unphysically distorted conformations, the issue can become serious for both database construction and the actual production simulation. In practice, it turns out that such traps cannot be removed trivially by merely supplying more data points, and thus an active filtering scheme should be adopted .…”

“…In practice, it turns out that such traps cannot be removed trivially by merely supplying more data points, and thus an active filtering scheme should be adopted . Nonetheless, for these practical issues, interpolation has the potential to become a very useful tool toward studying large systems especially when long simulation times are sought for . Thus, extending its capability to such a direction, namely, targeting a large system with long time simulations, will be an important step forward in its development.…”