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. 2009 Aug 27;109(15):3781.
doi: 10.1002/qua.22405.

A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems

Christina Bergonzo  1 , Arthur J Campbell, Ross C Walker, Carlos Simmerling
Affiliations

A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems

Christina Bergonzo et al. Int J Quantum Chem. .

Abstract

The nudged elastic band method (NEB) can be used to find a minimum energy path between two given starting structures. This method has been available in the standard release of the Amber9 and Amber10 suite of programs. In this paper a novel implementation of this method will be discussed, in which the nudged elastic band method is applied to only a specific, user-defined subset of atoms in a particular system, returning comparable results and minimum energy pathways as the standard implementation for an alanine dipeptide test system. This allows incorporation of explicit solvent with simulated systems, which may be preferred in many cases to an implicit solvent model. From a computational standpoint, this implementation of NEB also reduces the communication overhead inside the code, resulting in better performance for larger systems.

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Figures

Figure 1
Figure 1
The structure of alanine dipeptide. Rotation around the phi and psi angles dominates the energy landscape. Image generated with VMD 1.8.6.
Figure 2
Figure 2
The potential energy landscape for alanine dipeptide isomerization around the phi/psi dihedral angles. Minimum energy path for standard NEB implementation is shown using squares for each bead. Contours are shown at 2 kcal/mol intervals. The surface was generated by performing restrained minimizations at every 2° of the phi and psi angles.
Figure 3
Figure 3
Alanine dipeptide test systems: Alanine dipeptide in implicit solvent with a) NEB forces applied to all atoms b) NEB forces applied to atoms in orange. c) Alanine dipeptide in explicit solvent with NEB forces applied to atoms in orange. Images generated with VMD 1.8.6.
Figure 4
Figure 4
Potential energy surface of alanine dipeptide with minimum energy paths determined by a) standard NEB, b) PNEB in implicit solvent, and c) PNEB in explicit solvent. The minimum energy path is reproducible between all three systems.
Figure 5
Figure 5
a) Free energy profile in the region of the transition calculated using the PNEB path as a starting point. b) Full free energy surface of alanine dipeptide calculated by restrained umbrella sampling followed by 2D-WHAM. Boundary corresponding to a) is outlined in white to show similarity between calculated free energy using only the PNEB path and that calculated for the entire surface.
See this image and copyright information in PMC

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