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Calculation of free energy landscapes: A Histogram Reweighted Metadynamics approach [article]

Jens Smiatek, Andreas Heuer
2011 arXiv   pre-print
We present an efficient method for the calculation of free energy landscapes. Our approach involves a history dependent bias potential which is evaluated on a grid.  ...  The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Due to the presence of the bias potential, it can be also used to accelerate rare events.  ...  The authors also have to thank Vojtech Spiwok for using parts of his metadynamics source code available on his web page [91].  ... 
arXiv:1006.4308v2 fatcat:ud4a7wohujgyljb2m45tdy5gum

Free energy calculations of alanine tripeptide in explicit water using temperature accelerated sliced sampling

Anji Babu Kapakayala, Abhinav Gupta, Shivani Verma, Nisanth N. Nair
2019 Zenodo  
In this article, we demonstrate the application of this method in calculating free energy surface as a function of Ramachandran angles of alanine tripeptide in explicit water.  ...  The results of this work is of great importance as alanine tripeptide in solution is an ideal benchmark system for the methods to sample high dimensional free energy landscapes.  ...  HPC computational facilities at IIT Kanpur and Department of Chemistry are gratefully acknowledged.  ... 
doi:10.5281/zenodo.5644643 fatcat:2j4oqvu2nnf4rhy2xxarewk334

All-atom calculation of protein free-energy profiles

S. Orioli, A. Ianeselli, G. Spagnolli, P. Faccioli
2017 Journal of Chemical Physics  
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions  ...  the exact nature of the approach.  ...  ACKNOWLEDGMENTS We acknowledge funding by the Research Council of Norway (RCN) and the Fellows Initiative Natural Sciences (FINS).  ... 
doi:10.1063/1.5006039 pmid:29055321 fatcat:obm5tu3h5ve3ldcsioizwqybzi

Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface

Mingjun Yang, Lijiang Yang, Yiqin Gao, Hao Hu
2014 Journal of Chemical Physics  
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates.  ...  Therefore, the combined approach will become a very efficient method in the simulation of biomolecular processes which often involve sampling of complex rugged energy landscapes.  ...  ACKNOWLEDGMENTS We thank the Research Grants Council of Hong Kong, the University Development Fund on Fast Algorithms, Strategic Research Themes in Clean Energy and in Computation and Information, and  ... 
doi:10.1063/1.4887340 pmid:25084882 fatcat:wpywiewhrvdf3ghmd3x5lazqbq

Weighted force analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations [article]

Fabrizio Marinelli, José D. Faraldo-Gómez
2021 bioRxiv   pre-print
AbstractA methodology is proposed for calculating multidimensional free-energy landscapes of molecular systems, based on post-hoc analysis of multiple molecular dynamics trajectories wherein adaptive biases  ...  and show that calculated mean forces and free energies converge rapidly.  ...  Acknowledgements This work was funded by the Division of Intramural Research of the National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (USA).  ... 
doi:10.1101/2021.02.17.431654 fatcat:hbiagkdrwrcwdbbtaezbzos6ku

Mean Force Based Temperature Accelerated Sliced Sampling: Efficient Reconstruction of High Dimensional Free Energy Landscapes [article]

Asit Pal, Subhendu Pal, Shivani Verma, Motoyuki Shiga, Nisanth N. Nair
2021 arXiv   pre-print
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes.  ...  Application of the technique is demonstrated for alanine di- and tripeptides in vacuo to compute their two- and four-dimensional free energy landscapes, the latter of which is formidable in conventional  ...  In this respect, computing free energy landscape of such processes as a function of few collective variables (CVs) is a commonly employed strategy.  ... 
arXiv:2106.03321v1 fatcat:o2kuoxujpbaldm2lo3mk224upm

Learning free energy landscapes using artificial neural networks

Hythem Sidky, Jonathan K. Whitmer
2018 Journal of Chemical Physics  
ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.  ...  ability to efficiently conform to varied free energy landscapes.  ...  Similar to metadynamics, this approach relies on Gaussian representations of the free energy surface, with a focus on resolving low lying regions in higher dimensional free energy space.  ... 
doi:10.1063/1.5018708 pmid:29544298 fatcat:prdpflxyoffgtkia57477tgtdi

Global free energy landscapes as a smoothly joined collection of local maps [article]

F. Giberti, G. A. Tribello, M. Ceriotti
2020 arXiv   pre-print
The decomposition of the free-energy landscape in local basins can be updated iteratively as the simulation discovers new (meta)stable states.  ...  A well-tempered metadynamics-like bias is constructed as a function of these local variables.  ...  free-energy landscape.  ... 
arXiv:2011.07987v1 fatcat:cglaygjlrjadln7g47rtjaxtfa

Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics [article]

Pär Söderhjelm, Mandar Kulkarni
2021 bioRxiv   pre-print
Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues.  ...  The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.  ...  free energy landscape of residue F33 (blue).  ... 
doi:10.1101/2021.01.07.425261 fatcat:mwkjtf4x65awficzneeusrfocy

Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing [article]

Abhinav Gupta, Shivani Verma, Nisanth N. Nair
2020 arXiv   pre-print
Free energy barriers and free energies of high energy saddle points on the high dimensional free energy landscape of this system are reported.  ...  Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations.  ...  Acknowledgments Authors acknowledge the HPC facility (HPC2013) at the Indian Institute of Technology Kanpur. AG and SV thank the DST-INSPIRE for their Ph.D. fellowship.  ... 
arXiv:2010.01646v1 fatcat:vickxxzhgfhh3fzgoto46manf4

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc

Julien Michel, Rémi Cuchillo, Eugene A. Permyakov
2012 PLoS ONE  
An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers.  ...  and explicit solvent metadynamics molecular simulations.  ...  Niall Haslam and an anonymous reviewer for helpful comments on an earlier version of this manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0041070 pmid:22815918 pmcid:PMC3397933 fatcat:2abg7uhd2naqbdmzfcmyqpbp2a

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang, Tingjun Hou, James M. Briggs
2014 PLoS Computational Biology  
directly, and on the other hand, shortened the residence time induced by the flattened free energy surface.  ...  Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics  ...  Finally, the calculated free energy in each window could be integrated by reweighted method, such as weighted histogram analysis method (WHAM) [83, 84] , to give a total free energy change along the reaction  ... 
doi:10.1371/journal.pcbi.1003729 pmid:25033171 pmcid:PMC4102447 fatcat:rhbjtfhzmrhr3bw3rkswnelvei

Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration

Wei Chen, Andrew L. Ferguson
2018 Journal of Computational Chemistry  
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation.  ...  Our approach offers substantial speedups in exploration of configurational space, and is distinguished from exiting approaches by its capacity to simultaneously discover and directly accelerate along data-driven  ...  Weighted histogram analysis method (WHAM) Having conducted a series of umbrella sampling simulations tiling CV space, we estimate the unbiased free energy surface F (ξ) in these CVs by reweighting and  ... 
doi:10.1002/jcc.25520 pmid:30368832 fatcat:qfoasktcbvblnddigdvmxegmeu

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

G. A. Tribello, M. Ceriotti, M. Parrinello
2012 Proceedings of the National Academy of Sciences of the United States of America  
In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes.  ...  We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.  ...  The authors would like to thank Davide Branduardi and Giovanni Bussi for useful discussions along with Ali Hassanali and Federico Giberti for reading early drafts of the manuscript and giving suggestions  ... 
doi:10.1073/pnas.1201152109 pmid:22427357 pmcid:PMC3325650 fatcat:q7p5izicqrgx3iol4fdymqkoju

Riemann metric approach to optimal sampling of multidimensional free-energy landscapes

Viveca Lindahl, Jack Lidmar, Berk Hess
2018 Physical review. E  
We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by  ...  Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses.  ...  The "flat" target distribution (5) is arguably a good choice if all points of Λ in the free-energy landscape are of equal interest, but this is seldom the case.  ... 
doi:10.1103/physreve.98.023312 fatcat:hcst7z7pf5d7dda2nerc453h2m
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