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Article: Reversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation)

TitleReversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation)
Authors
KeywordsAccuracy
Ewald Summation
Free Energy
Integration Method
Molecular Dynamics
Slow Growth
Issue Date2002
PublisherTaylor & Francis Ltd. The Journal's web site is located at http://www.tandf.co.uk/journals/titles/08927022.asp
Citation
Molecular Simulation, 2002, v. 28 n. 1-2, p. 67-80 How to Cite?
AbstractWe review the slow-growth method for computing free energy changes for processes in conformation space or in "chemical" space, in which a system parameter, x is changed at each integration time step, and the free energy, ΔA is approximated by accumulating the work performed at each step. The method is simple to implement and use, convergence can be monitored by performing longer simulations and by performing the simulations changing x in both directions, and statistical error can be evaluated by performing multiple independent simulations. Because slow growth simulates a continuous process, it closely approximates the ideal isothermal quasi-static process used in defining the free energy in thermodynamics, and thus a small hysteresis in slow-growth results practically guarantees that the process is reversible, which is of course a prerequisite for the results to represent a free energy change. Whenever hysteresis is not negligible (which happens when the required long simulation times are unattainable), Boltzmann exponential averaging of slow growth results should be used to produce an upper bound on the free energy change (Jarzynski, C., Phys. Rev. Lett., 78, 2690-2693, 1997), with exponential averaging of results for change in the opposite direction giving a lower bound; it is then reasonable to choose the mean of the bounds as the best estimate. The work, W sg for transfer of benzamidine from water to vacuum has been computed by insertion and extraction simulations, at different switching times. (As implemented, the molecular transformation calculation requires two evaluations of the Ewald sum; the increase in computer time required for this has been reduced by use of a multiple time step scheme in which the Ewald summations are executed at intervals of several integration time steps.) For the longest switching time, the distribution of values of W sg is narrow, hysteresis is small and all methods produce a similar result for ΔA, As the switching time is reduced, (i) the distribution becomes non-Gaussian, (ii) the frictional portions and the distributions for insertion and extraction differ, (iii) the mean of the linear averages and the mean of the exponential averages for insertion and extraction both fail to give an accurate estimate of ΔA. © 2002 Taylor & Francis Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/167825
ISSN
2015 Impact Factor: 1.678
2015 SCImago Journal Rankings: 0.535
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHu, Hen_US
dc.contributor.authorYun, RHen_US
dc.contributor.authorHermans, Jen_US
dc.date.accessioned2012-10-08T03:12:00Z-
dc.date.available2012-10-08T03:12:00Z-
dc.date.issued2002en_US
dc.identifier.citationMolecular Simulation, 2002, v. 28 n. 1-2, p. 67-80en_US
dc.identifier.issn0892-7022en_US
dc.identifier.urihttp://hdl.handle.net/10722/167825-
dc.description.abstractWe review the slow-growth method for computing free energy changes for processes in conformation space or in "chemical" space, in which a system parameter, x is changed at each integration time step, and the free energy, ΔA is approximated by accumulating the work performed at each step. The method is simple to implement and use, convergence can be monitored by performing longer simulations and by performing the simulations changing x in both directions, and statistical error can be evaluated by performing multiple independent simulations. Because slow growth simulates a continuous process, it closely approximates the ideal isothermal quasi-static process used in defining the free energy in thermodynamics, and thus a small hysteresis in slow-growth results practically guarantees that the process is reversible, which is of course a prerequisite for the results to represent a free energy change. Whenever hysteresis is not negligible (which happens when the required long simulation times are unattainable), Boltzmann exponential averaging of slow growth results should be used to produce an upper bound on the free energy change (Jarzynski, C., Phys. Rev. Lett., 78, 2690-2693, 1997), with exponential averaging of results for change in the opposite direction giving a lower bound; it is then reasonable to choose the mean of the bounds as the best estimate. The work, W sg for transfer of benzamidine from water to vacuum has been computed by insertion and extraction simulations, at different switching times. (As implemented, the molecular transformation calculation requires two evaluations of the Ewald sum; the increase in computer time required for this has been reduced by use of a multiple time step scheme in which the Ewald summations are executed at intervals of several integration time steps.) For the longest switching time, the distribution of values of W sg is narrow, hysteresis is small and all methods produce a similar result for ΔA, As the switching time is reduced, (i) the distribution becomes non-Gaussian, (ii) the frictional portions and the distributions for insertion and extraction differ, (iii) the mean of the linear averages and the mean of the exponential averages for insertion and extraction both fail to give an accurate estimate of ΔA. © 2002 Taylor & Francis Ltd.en_US
dc.languageengen_US
dc.publisherTaylor & Francis Ltd. The Journal's web site is located at http://www.tandf.co.uk/journals/titles/08927022.aspen_US
dc.relation.ispartofMolecular Simulationen_US
dc.subjectAccuracyen_US
dc.subjectEwald Summationen_US
dc.subjectFree Energyen_US
dc.subjectIntegration Methoden_US
dc.subjectMolecular Dynamicsen_US
dc.subjectSlow Growthen_US
dc.titleReversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation)en_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1080/08927020211971en_US
dc.identifier.scopuseid_2-s2.0-0042531222en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0042531222&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume28en_US
dc.identifier.issue1-2en_US
dc.identifier.spage67en_US
dc.identifier.epage80en_US
dc.identifier.isiWOS:000176122400006-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridYun, RH=6701325409en_US
dc.identifier.scopusauthoridHermans, J=7201896483en_US

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