Comparison Between Mean Forces and Swarms-of-Trajectories String Methods

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2015 Nov 19

PMID 26580029

Citations 20

Authors

Luca Maragliano

Benoit Roux

Eric Vanden-Eijnden

Affiliations

Soon will be listed here.

Abstract

The original formulation of the string method in collective variable space is compared with a recent variant called string method with swarms-of-trajectories. The assumptions made in the original method are revisited and the significance of the minimum free energy path (MFEP) is discussed in the context of reactive events. These assumptions are compared to those made in the string method with swarms-of-trajectories, and shown to be equivalent in a certain regime: in particular an expression for the path identified by the swarms-of-trajectories method is given and shown to be closely related to the MFEP. Finally, the algorithmic aspects of both methods are compared.

Citing Articles

Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String.

Jia X, Xin Z, Fu Y, Duan H Molecules. 2024; 29(20).

PMID: 39459188 PMC: 11510520. DOI: 10.3390/molecules29204819.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M J Phys Chem B. 2024; 128(41):9976-10042.

PMID: 39303207 PMC: 11492285. DOI: 10.1021/acs.jpcb.4c04100.

Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.

Niu S, Ren F Molecules. 2024; 29(11).

PMID: 38893427 PMC: 11173574. DOI: 10.3390/molecules29112549.

A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.

Blanc F, Houdusse A, Cecchini M PLoS Comput Biol. 2024; 20(4):e1012005.

PMID: 38662764 PMC: 11086841. DOI: 10.1371/journal.pcbi.1012005.

Experimental and Theoretical Investigation of External Electric-Field-Induced Crystallization of TKX-50 from Solution by Finite-Temperature String with Order Parameters as Collective Variables for Ionic Crystals.

Ren F, Wang X, Zhang Q, Wang X, Chang L, Zhang Z Molecules. 2024; 29(5).

PMID: 38474669 PMC: 10934131. DOI: 10.3390/molecules29051159.

References

Kirmizialtin S, Nguyen V, Johnson K, Elber R . How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure. 2012; 20(4):618-27. PMC: 3322391. DOI: 10.1016/j.str.2012.02.018. View

Ovchinnikov V, Karplus M, Vanden-Eijnden E . Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys. 2011; 134(8):085103. PMC: 3060930. DOI: 10.1063/1.3544209. View

E W, Ren W, Vanden-Eijnden E . Finite temperature string method for the study of rare events. J Phys Chem B. 2006; 109(14):6688-93. DOI: 10.1021/jp0455430. View

Lacroix J, Pless S, Maragliano L, Campos F, Galpin J, Ahern C . Intermediate state trapping of a voltage sensor. J Gen Physiol. 2012; 140(6):635-52. PMC: 3514728. DOI: 10.1085/jgp.201210827. View

Pan A, Sezer D, Roux B . Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B. 2008; 112(11):3432-40. PMC: 2757167. DOI: 10.1021/jp0777059. View

MacKerell A, Bashford D, Bellott M, Dunbrack R, Evanseck J, Field M . All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 2014; 102(18):3586-616. DOI: 10.1021/jp973084f. View

Bolhuis P, Chandler D, Dellago C, Geissler P . Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem. 2002; 53:291-318. DOI: 10.1146/annurev.physchem.53.082301.113146. View

Krivov S . The free energy landscape analysis of protein (FIP35) folding dynamics. J Phys Chem B. 2011; 115(42):12315-24. DOI: 10.1021/jp208585r. View

Gan W, Yang S, Roux B . Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophys J. 2009; 97(4):L8-L10. PMC: 2726321. DOI: 10.1016/j.bpj.2009.06.016. View

10.

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A . Minimum free energy path of ligand-induced transition in adenylate kinase. PLoS Comput Biol. 2012; 8(6):e1002555. PMC: 3369945. DOI: 10.1371/journal.pcbi.1002555. View

11.

Best R, Hummer G, Eaton W . Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A. 2013; 110(44):17874-9. PMC: 3816414. DOI: 10.1073/pnas.1311599110. View

12.

Vashisth H, Abrams C . All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element. Proteins. 2013; 81(6):1017-30. DOI: 10.1002/prot.24255. View

13.

Jo S, Rui H, Lim J, Klauda J, Im W . Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B. 2010; 114(42):13342-8. DOI: 10.1021/jp108166k. View

14.

Johnson M, Hummer G . Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. J Phys Chem B. 2012; 116(29):8573-83. PMC: 3406241. DOI: 10.1021/jp212611k. View

15.

Ciccotti G, Kapral R, Vanden-Eijnden E . Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics. Chemphyschem. 2005; 6(9):1809-14. DOI: 10.1002/cphc.200400669. View

16.

Zhu F, Hummer G . Pore opening and closing of a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A. 2010; 107(46):19814-9. PMC: 2993413. DOI: 10.1073/pnas.1009313107. View

17.

Maragliano L, Fischer A, Vanden-Eijnden E, Ciccotti G . String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys. 2006; 125(2):24106. DOI: 10.1063/1.2212942. View

18.

Maragliano L, Vanden-Eijnden E . Single-sweep methods for free energy calculations. J Chem Phys. 2008; 128(18):184110. DOI: 10.1063/1.2907241. View

19.

Bolhuis P, Dellago C, Chandler D . Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci U S A. 2000; 97(11):5877-82. PMC: 18527. DOI: 10.1073/pnas.100127697. View

20.

Vashisth H, Maragliano L, Abrams C . "DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop. Biophys J. 2012; 102(8):1979-87. PMC: 3328698. DOI: 10.1016/j.bpj.2012.03.031. View