Table of Contents
ISRN Computational Biology
Volume 2013 (2013), Article ID 640125, 5 pages
http://dx.doi.org/10.1155/2013/640125
Research Article

Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures

1Compugen Ltd., 69512 Tel Aviv, Israel
2The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University , 52900 Ramat-Gan, Israel

Received 31 January 2013; Accepted 25 February 2013

Academic Editors: F. Barbault and F. Fanelli

Copyright © 2013 Ifat Shub et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications.