Paper Citing NAMD - Abstract
Branduardi, Davide; Faraldo-Gomez, Jose D.
String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:4140-4154, SEP 2013
The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a predefined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a nontrivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method, we analyze the isomerization of the alanine dipeptide in a vacuum and the chair-to-inverted-chair transition of beta-D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of the isomerization process are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields near-identical minimum free-energy paths and committor distributions to those obtained via a highly dimensional string.
