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Register a new userEnhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering
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The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.
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We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global conformational space by exchanging the corresponding parts between a pair of conformations of a protein. In this study, we applied this method to an $alpha$-helical protein, Trp-cage mini protein, which has 20 amino-acid residues. The conformations obtained from the simulations are in good agreement with the experimental results.
We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters for temperature-update and pressure-update are self-updated independently according to the trapezoidal rule. In order to test the effectiveness of the algorithm, we applied our proposed method to a peptide, chignolin, in explicit water. After setting all weight parameters to zero, the weight parameters were quickly determined during the simulation. The simulation realised a uniform random walk in the entire temperature-pressure space.
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective variables has proven challenging. Here we suggest that the NMR $S^2$ order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between $S^2$ and entropy. Using the $S^2$ order parameter and a surrogate for the protein enthalpy in conjunction with Metadynamics or Variationally Enhanced Sampling we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. From a more conceptual point of view this implies describing folding as a resulting from a trade off between entropy and enthalpy. We also use $S^2$ in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.
We show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the concept of effective energy introduced in a recent paper [J. Chem. Phys. 126, 014101 (2007)]. Our integrator leads to correct sampling also in the difficult high-friction limit. We also show how these ideas can be applied in practical simulations, using a Lennard-Jones crystal as a paradigmatic case.
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to learn collective variables with a multitask neural network, where a common upstream part reduces the high dimensionality of atomic configurations to a low dimensional latent space, and separate downstream parts map the latent space to predictions of basin class labels and potential energies. The resulting latent space is shown to be an effective low-dimensional representation, capturing the reaction progress and guiding effective umbrella sampling to obtain accurate free energy landscapes. This approach is successfully applied to model systems including a 5D Muller Brown model, a 5D three-well model, and alanine dipeptide in vacuum. This approach enables automated dimensionality reduction for energy controlled reactions in complex systems, offers a unified framework that can be trained with limited data, and outperforms single-task learning approaches, including autoencoders.
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