Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations
✍ Scribed by Yong Duan; Shankar Kumar; John M. Rosenberg; Peter A. Kollman
- Publisher
- John Wiley and Sons
- Year
- 1995
- Tongue
- English
- Weight
- 451 KB
- Volume
- 16
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
Current macromolecular energy minimization algorithms become inefficient and prone to failure when bond length constraints are imposed. They are required to relieve steric stresses in biomolecules prior to a molecular dynamics simulation. Unfortunately, the latter often require constraints, leading to difficulties in initiating trajectories from unconstrained energy minima. This difficulty was overcome by requiring that the components of the energy gradient vanish along the constrained bonds. The modified energy minimization algorithm converges to a lower energy in a fewer number of iterations and is more robust than current implementations. The method has been successfully applied to the Dickerson DNA dodecamer, CGCGAA'ITCGCG. 0 1995 by John Wiley & Sons, Inc.
techniques' are routinely used in X-ray diffraction studies of proteins and DNA to adjust bond lengths, bond angles, etc. so that they conform to known stereochemical values. They have been used extensively in the parameterization of molecular mechanics force fields's3 and in molecular dynambiomolecules, in which the stresses in the molecule lar structure and function. Gradient minimization ics (MD) and Monte Carlo (MC) studies of generally must be prior to the commencement of the simulation^^,^ and in which, for large