Abstract
One of the challenges in the large scale simulations required for biomolecular system is the recording, monitoring and visualization of configurational information from molecular dynamics trajectories. A detailed record of instantaneous configuration along the full trajectory can quickly become unmanageable. In this paper we will describe an alternative approach where configurations averaged over trajectory segments are used to follow the detailed molecular behaviour of a system over multiple-nanosecond simulations. We will then discuss the successful application of this approach to molecular dynamics simulations of crystal growth.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bergethon, P.R.: The Physical Basis of Biochemistry: The Foundations of Molecular Biophysics. Springer, Heidelberg (2000)
Becker, O.M., MacKerell, A.D., Roux Jr., B., Watanabe, M.: Computational Biochemistry and Biophysics, Marcel Dekker, USA (2001)
Lyubartsev, A.P., Karttunen, M., Vattulainen, I., Laaksonen, A.: Soft Mater. 1, 121–137 (2003)
Nielsen, S.O., Lopez, C.F., Srinivas, G., Klein, M.L.: J. of Phys.: Cond. Matter 16, R481–R512 (2004)
Ortiz, V., Nielsen, S.O., Klein, M.L., Discher, D.E.: J. of Polymer Sc., B: Polymer Phys. 44, 1907–1918 (2006)
Srinivas, G., Discher, D.E., Klein, M.L.: Nature Materials 3, 638–644 (2004)
de la Peña, L.H., Kusalik, P.G.: Mol. Phys. 102, 927–937 (2004)
Steinhardt, P.J., Nelson, D.R., Ronchetti, M.: Phys. Rev. B 28, 784 (1983)
ten Wolde, P.R., Ruiz-Montero, M.J., Frenkel, D.: Phys. Rev. Lett. 75, 2714 (1995)
ten Wolde, P.R., Ruiz-Montero, M.J., Frenkel, D.: J. Chem. Phys. 104, 9932 (1996)
Desgranges, C., Delhommelle, J.: J. Am. Chem. Soc. 128, 10368–10369 (2006)
Razul, M.S.G., Tam, E.V., Lam, M.E., Kusalik, P.G.: Mol. Phys, 103, 1929 (2005)
Razul, M.S.G., Hendry, J.G., Kusalik, P.G.: J. Chem. Phys. 123, 204722 (2005)
Vatamanu, J., Kusalik, P.G.: J. Phys. Chem. B. 110, 15896 (2006)
Vatamanu, J., Kusalik, P.G.: J. Chem. Phys. (accepted)
Vatamanu, J., Kusalik, P.G.: J. Am. Chem. Soc. 128, 15588 (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Gillis, K., Vatamanu, J., Razul, M.S.G., Kusalik, P.G. (2007). Averaged Configurations from Molecular Dynamics Simulations. In: Kågström, B., Elmroth, E., Dongarra, J., Waśniewski, J. (eds) Applied Parallel Computing. State of the Art in Scientific Computing. PARA 2006. Lecture Notes in Computer Science, vol 4699. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75755-9_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-75755-9_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75754-2
Online ISBN: 978-3-540-75755-9
eBook Packages: Computer ScienceComputer Science (R0)