ILVES: Accurate and Efficient Bond Length and Angle Constraints in Molecular Dynamics.

ABSTRACT: All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation time scales increase, so does the associated computational cost. To extend simulated time using the same resources, a common strategy is to constrain the fastest degrees of freedom, such as bond lengths, allowing for larger integration time steps without compromising accuracy. The de facto state-of-the-art algorithms for this purpose─SHAKE, LINCS, and P-LINCS─are integrated into most molecular dynamics packages and widely adopted across the field. Despite their impact, these methods exhibit limitations: all converge slowly when high numerical accuracy is r

SUBMITTER: Lopez-Villellas L 

PROVIDER: S-EPMC12461920 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature