Kirkwood–Buff theory of molecular and protein association, aggregation, and cellular crowding
An analysis of the effect of a cosolvent on the association of a solute in solution using the Kirkwood–Buff theory of solutions is presented. The approach builds on the previous results of Ben-N...
An analysis of the effect of a cosolvent on the association of a solute in solution using the Kirkwood–Buff theory of solutions is presented. The approach builds on the previous results of Ben-N...
Folding simulations of gramicidin A into the 
-helix conformations: Simulated annealing molecular dynamics study
Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the 6.3-helix, to act as a cation-selective ion...
-helix conformations: Simulated annealing molecular dynamics studyGramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the 6.3-helix, to act as a cation-selective ion...
Error and efficiency of replica exchange molecular dynamics simulations
J. Chem. Phys. 131, 165102 (2009); doi:10.1063/1.3249608
Published 27 October 2009
You are not logged in to this journal. Log in
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water.
| History: | Received 24 July 2009; accepted 25 September 2009; published 27 October 2009 |
| Permalink: |
http://link.aip.org/link/?JCPSA6/131/165102/1 |
| BUY THIS ARTICLE | (US$24) |
|
|
|
|
Connotea
CiteULike
del.icio.us
BibSonomy
REFERENCES (30)
For access to fully linked references, you need to log in.
For access to fully linked references, you need to Log in.
- Y. Sugita and Y. Okamoto,
Chem. Phys. Lett. 314, 141 (1999) . - A. E. García and K. Y. Sanbonmatsu,
Proc. Natl. Acad. Sci. U.S.A. 99, 2782 (2002) . - C. J. Geyer, Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface (American Statistical Association, New York, 1991), pp. 156–163.
- K. Hukushima and K. Nemoto,
J. Phys. Soc. Jpn. 65, 1604 (1996) . - C. H. Bennett,
J. Comput. Phys. 22, 245 (1976) . - R. H. Swendsen and J. -S. Wang, Phys. Rev. Lett. 57, 2607 (1986).
- E. Rosta, N. -V. Buchete, and G. Hummer,
J. Chem. Theory Comput. 5, 1393 (2009) . - D. Sindhikara, Y. L. Meng, and A. E. Roitberg, J. Chem. Phys. 128, 024103 (2008).
- W. Zheng, M. Andrec, E. Gallicchio, and R. M. Levy,
Proc. Natl. Acad. Sci. U.S.A. 104, 15340 (2007) . - W. Zheng, M. Andrec, E. Gallicchio, and R. M. Levy,
J. Phys. Chem. B 112, 6083 (2008) . - S. Trebst, M. Troyer, and U. H. E. Hansmann, J. Chem. Phys. 124, 174903 (2006).
- J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007).
- W. Nadler and U. H. E. Hansmann, Phys. Rev. E 75, 026109 (2007).
- W. Nadler and U. H. E. Hansmann, Phys. Rev. E 76, 065701 (2007).
- W. Nadler and U. H. E. Hansmann,
J. Phys. Chem. B 112, 10386 (2008) . - H. Nymeyer,
J. Chem. Theory Comput. 4, 626 (2008) . - M. J. Abraham and J. E. Gready,
J. Chem. Theory Comput. 4, 1119 (2008) . - R. Denschlag, M. Lingenheil, and P. Tavan,
Chem. Phys. Lett. 458, 244 (2008) . - C. Zhang and J. Ma, J. Chem. Phys. 129, 134112 (2008).
- W. Y. Yang and M. Gruebele,
Biochemistry 43, 13018 (2004) . - I. -C. Yeh and G. Hummer,
Biophys. J. 86, 681 (2004) . - M. Boguna, A. M. Berezhkovskii, and G. H. Weiss,
J. Phys. Chem. A 105, 4898 (2001) . - A. M. Berezhkovskii, A. Szabo, and G. H. Weiss, J. Chem. Phys. 110, 9145 (1999).
- R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, New York, 2001).
- D. J. Bicout and A. Szabo, J. Chem. Phys. 109, 2325 (1998).
- G. Lipari and A. Szabo,
J. Am. Chem. Soc. 104, 4546 (1982) . - R. Denschlag, M. Lingenheil, and P. Tavan,
Chem. Phys. Lett. 473, 193 (2009) . - N. V. Buchete and G. Hummer, Phys. Rev. E 77, 030902 (2008).
- N. V. Buchete and G. Hummer,
J. Phys. Chem. B 112, 6057 (2008) . - P. Liu, B. Kim, R. A. Friesner, and B. J. Berne,
Proc. Natl. Acad. Sci. U.S.A. 102, 13749 (2005) .
