Paper Citing NAMD - Abstract
Grebner, Christoph; Kaestner, Johannes; Thiel, Walter; Engels, Bernd
A New Tabu-Search-Based Algorithm for Solvation of Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:814-821, JAN 2013
The proper description of explicit water shells is of enormous importance for all-atom calculations. We propose a new approach for the setup of water shells around proteins based on Tabu-Search global optimization and compare its efficiency with standard molecular dynamics protocols using the chignolin protein as a test case. Both algorithms generate reasonable water shells, but the new approach provides solvated systems with an increased water-enzyme interaction and offers further advantages. It enables a stepwise buildup of the solvent shell, so that the more important inner part can be prepared more carefully. It also allows the generation of solute structures which can be biased either toward the (experimental) starting structure or the underlying theoretical model, i.e., the employed force field.
