A simulation method of combinding boundary element method with generalized Langevin dynamics
- 30 Downloads
A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.
Keywordspotential of mean force of solvent boundary element method friction memory function generalized Langevin dynamics
Unable to display preview. Download preview PDF.
- 3.van Gunsteren. W. F., Weiner, P. K., Wilkinson, A., J. Computer Simulation of Biomolecular System: Theoretical and Experimental Application. Vol. 2. The Netherlands: Leidon ESCOM, 1993.Google Scholar
- 10.Wang, C. X., Wan, S. Z., Xiang Z. X. et al., Incorporating hydration force determined by boundary element method into stochastic dynamics, J. Phys. Chem., 1997, 102: 230.Google Scholar
- 15.van Gunsteren. W. F., Berendsen, H. J. C., Groningen Molecular Simulation (GROMOS) Library Manual, Groningen: Biomos, 1987.Google Scholar