期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 11, 期 12, 页码 5947-5960出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.5b00749
关键词
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资金
- ERC [307494-pcCell]
- Deutsche Forschungsgemeinschaft [825/3-1]
- National Science Foundation [CHE-1152344, CHE-1265929]
- Welch foundation [C-1570]
- EPSRC [EP/K039512/1]
- Data Analysis and Visualization Cyber Infrastructure - NSF [OCI-0959097]
- NIH [NCRR S10RR02950]
- IBM Shared University Research (SUR) Award
- CISCO
- Qlogic
- Adaptive Computing
- EPSRC [EP/K039512/1] Funding Source: UKRI
- Engineering and Physical Sciences Research Council [EP/K039512/1] Funding Source: researchfish
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1265929] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Physics [1427654] Funding Source: National Science Foundation
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [1152344] Funding Source: National Science Foundation
Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.
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