Abstract
In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.
Similar content being viewed by others
References
G. Grest, K. Kremer, Phys. Rev. A 33, 3628 (1986)
K. Kremer, G. Grest, I. Carmesin, Phys. Rev. Lett. 61, 566 (1988)
L. Yelash, M. Müller, W. Paul, K. Binder, J. Chem. Theory Comput. 2, 588 (2006)
T. Spyriouni, C. Tzoumanekas, D. Theodorou, F. Müller-Plathe, G. Milano, Macromolecules 40, 3876 (2007)
J. McCammon, M. Karplus, Nature 268, 765 (1977)
M. Karplus, J. McCammon, Nature 277, 578 (1979)
P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti, M. Parrinello, J. Phys. Chem. B 110, 3533 (2006)
H. Lou, R.I. Cukier, J. Phys. Chem. B 110, 12796 (2006)
K. Arora, C.L. Brooks, Proc. Natl. Acad. Sci. USA 104, 18496 (2007)
F. Pontiggia, A. Zen, C. Micheletti, Biophys. J 95, 5901 (2008)
M.M. Tirion, D. ben Avraham, J. Mol. Biol. 230, 186 (1993)
M.M. Tirion, Phys. Rev. Lett. 77, 1905 (1996)
I. Bahar, A.R. Atilgan, B. Erman, Folding Design 2, 173 (1997)
C. Micheletti, P. Carloni, A. Maritan, Proteins 55, 635 (2004)
R. Potestio, F. Pontiggia, C. Micheletti, Biophys. J 96, 4993 (2009)
C. Globisch, V. Krishnamani, M. Deserno, C. Peter, PLoS ONE 8, e60582 (2013)
K. Kremer, Computer simulations in soft matter science, Vol. 53 (IOP Publishing Ltd., 2000), p. 145
K. Kremer, F. Müller-Plathe, MRS Bulletin 26, 205 (2001)
N.A. van der Vegt, C. Peter, K. Kremer, Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations, (CRC Press – Taylor and Francis Group, 2009), p. 379
C. Hijón, E. Vanden-Eijnden, R. Delgado-Buscalioni, P. Español, Farad. Discuss. 144, 301 (2010)
W. Noid, Systematic methods for structurally consistent coarse-grained models, Vol. 924 (Humana Press, 2013), p. 487
W.G. Noid, J. Chem. Phys. 139, 090901 (2013)
M. Praprotnik, L. Delle Site, K. Kremer, J. Chem. Phys. 123, 224106 (2005)
M. Praprotnik, L. Delle Site, K. Kremer, Phys. Rev. E. 73, 066701 (2006)
M. Praprotnik, L. Delle Site, K. Kremer, J. Chem. Phys. 126, 134902 (2007)
M. Praprotnik, L. Delle Site, K. Kremer, Ann. Rev. Phys. Chem. 59, 545 (2008)
S. Fritsch, C. Junghans, K. Kremer, J. Chem. Theory Comput. 8, 398 (2012)
A.B. Poma, L.D. Site, Phys. Rev. Lett. 104, 250201 (2010)
R. Potestio, L. Delle Site, J. Chem. Phys. 136, 054101 (2012)
B. Ensing, S. Nielsen, P. Moore, M. Klein, M. Parrinello, J. Chem. Theor. Comp. 3, 1100 (2007)
M. Praprotnik, S. Poblete, L. Delle Site, K. Kremer, Phys. Rev. Lett. 107, 099801 (2011)
S. Fritsch, S. Poblete, C. Junghans, G. Ciccotti, L. Delle Site, K. Kremer, Phys. Rev. Lett. 108, 170602 (2012)
R. Potestio, S. Fritsch, P. Español, R. Delgado-Buscalioni, K. Kremer, R. Everaers, D. Donadio, Phys. Rev. Lett. 110, 108301 (2013)
R. Potestio, P. Español, R. Delgado-Buscalioni, R. Everaers, K. Kremer, D. Donadio, Phys. Rev. Lett. 111, 060601 (2013)
A. Agarwal, H. Wang, C. Schütte, L.D. Site, J. Chem. Phys. 141, 034102 (2014)
K. Kreis, D. Donadio, K. Kremer, R. Potestio, Europhys. Lett. 108, 30007 (2014)
P. Español, R. Delgado-Buscalioni, R. Everaers, R. Potestio, D. Donadio, K. Kremer, J. Chem. Phys. 142, 064115 (2015)
B. Mukherjee, L. Delle Site, K. Kremer, C. Peter, J. Phys. Chem. B. 116, 8474 (2012)
B. Mukherjee, C. Peter, K. Kremer, Phys. Rev. E. 88, 010502 (2013)
D. Reith, M. Putz, F. Müller-Plathe, J. Comp. Chem. 24, 1624 (2003)
H. Wang, C. Junghans, K. Kremer, Eur. Phys. J. E 28, 221 (2009)
L. Delle Site, Phys. Rev. E. 76, 047701 (2007)
H. Wang, C. Hartmann, C. Schütte, L. Delle Site, Phys. Rev. X 3, 011018 (2013)
J. Kirkwood, J. Chem. Phys. 3, 300 (1935)
J.D. Halverson, T. Brandes, O. Lenz, A. Arnold, S. Bevc, V. Starchenko, K. Kremer, T. Stühn, D. Reith, Comput. Phys. Commun. 184, 1129 (2013)
H. Berendsen, J. Grigera, T. Straatsma, J. Phys. Chem. 91, 6269 (1987)
S. Miyamoto, P.A. Kollman, J. Comput. Chem. 13, 952 (1992)
D. Mukherji, N.F.A. van der Vegt, K. Kremer, L. Delle Site, J. Chem. Theory Comput. 8, 375 (2012)
V. Rühle, C. Junghans, A. Lukyanov, K. Kremer, D. Andrienko, J. Chem. Theory Comput. 5, 3211 (2009)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kreis, K., Fogarty, A.C., Kremer, K. et al. Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations. Eur. Phys. J. Spec. Top. 224, 2289–2304 (2015). https://doi.org/10.1140/epjst/e2015-02412-1
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1140/epjst/e2015-02412-1