CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4446
Abstract: Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM‐GUI… read more here.
Keywords: gui enhanced; enhanced sampling; enhanced sampler; charmm gui ... See more keywords
Extraction of new super-Gaussian solitons via collective variables
Sign Up to like & getrecommendations! Published in 2021 at "Optical and Quantum Electronics"
DOI: 10.1007/s11082-021-03125-1
Abstract: The present study implements the collective variable (CV) approach to examine an important Schrodinger equation known as the Fokas-Lenells equation which expresses the dynamics of solitons for optical fibers in terms of pulse parameters known… read more here.
Keywords: pulse parameters; extraction new; new super; gaussian solitons ... See more keywords
DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00883
Abstract: We present Deep learning for Collective Variables (DeepCV), a computer code that provides an efficient and customizable implementation of the deep autoencoder neural network (DAENN) algorithm that has been developed in our group for computing… read more here.
Keywords: deepcv deep; collective variables; deep learning; framework ... See more keywords
Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.0c00981
Abstract: With the continual improvement of computing hardware and algorithms, simulations have become a powerful tool for understanding all sorts of (bio)molecular processes. To handle the large simulation data sets and to accelerate slow, activated transitions,… read more here.
Keywords: network; neural networks; cvs; genetic algorithms ... See more keywords
Constructing Collective Variables Using Invariant Learned Representations.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00729
Abstract: On the time scales accessible to atomistic numerical modeling, chemical reactions are considered rare events. Therefore, the atomistic simulations are commonly biased along a low-dimensional representation of a chemical reaction in an atomic structure space,… read more here.
Keywords: constructing collective; learned representations; variables using; collective variables ... See more keywords
Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00873
Abstract: Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of such enhanced sampling methods… read more here.
Keywords: learning collective; enhanced sampling; reweighted manifold; manifold learning ... See more keywords
Collective Variables for Crystallization Simulations—from Early Developments to Recent Advances
Sign Up to like & getrecommendations! Published in 2022 at "ACS Omega"
DOI: 10.1021/acsomega.2c06310
Abstract: Crystallization is an important physicochemical process which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental symmetry-breaking transition. While experiments provide equilibrium… read more here.
Keywords: crystallization simulations; collective variables; crystallization; variables crystallization ... See more keywords
Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.
Sign Up to like & getrecommendations! Published in 2022 at "Soft matter"
DOI: 10.1039/d2sm00888b
Abstract: The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in biomolecular systems. Due to long time scales involved in the transition, it is challenging to study… read more here.
Keywords: umbrella sampling; finite temperature; temperature string; collective variables ... See more keywords
Critical comparison of general-purpose collective variables for crystal nucleation.
Sign Up to like & getrecommendations! Published in 2023 at "Physical review. E"
DOI: 10.1103/physreve.107.l012601
Abstract: The nucleation of crystals is a prominent phenomenon in science and technology that still lacks a full atomic-scale understanding. Much work has been devoted to identifying order parameters able to track the process, from the… read more here.
Keywords: comparison general; purpose collective; critical comparison; variables crystal ... See more keywords
Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations.
Sign Up to like & getrecommendations! Published in 2017 at "Physical review letters"
DOI: 10.1103/physrevlett.119.015701
Abstract: Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is… read more here.
Keywords: drive crystallization; crystallization; collective variables; enthalpy fluctuations ... See more keywords
Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Sign Up to like & getrecommendations! Published in 2019 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2019.00025
Abstract: The state of a molecular system can be described in terms of collective variables. These low-dimensional descriptors of molecular structure can be used to monitor the state of the simulation, to calculate free energy profiles… read more here.
Keywords: analysis; approximation complex; complex collective; collective variables ... See more keywords