We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number of time-steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). We illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster.
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an efficient strategy for sampling molecular systems characterized by rare events, which we call learned replica exchange (LREX). In LREX, a normalizing flow is trained to map the configurations of the fastest-mixing replica into configurations belonging to the target distribution, allowing direct exchanges between the two without the need to simulate intermediate replicas. This can significantly reduce the computational c…
We estimated the residual entropy of ice Ih by the recently developed simulation protocol, namely, the combination of Replica-Exchange Wang-Landau algorithm and Multicanonical Replica-Exchange Method. We employed a model with the nearest neighbor interactions on the three-dimensional hexagonal lattice, which satisfied the ice rules in the ground state. The results showed that our estimate of the residual entropy is found to be within 0.038 % of series expansion estimate by Nagle and within 0.000077 % of PEPS algorithm by Vanderstraeten. In this article, we not only give our latest estimate of …
Generative Replica-Exchange: A Flow-based Framework for Accelerating Replica Exchange Simulations
State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University（生物活性分子与药物性评估国家重点实验室，中国传统医药现代化与创新药物发现国际合作实验室，中国教育部（MOE）药学院，暨南大学）；Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine（生物化学与分子药理学系，纽约大学格罗斯曼医学院）；Howard Hughes Medical Institute, NYU Grossman School of Medicine（霍华德·休斯医学研究所，纽约大学格罗斯曼医学院）；Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology（理论化学与生物学系，皇家理工学院（KTH））
We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will re…
In replica exchange Monte Carlo (REM), tuning of the temperature set and the exchange scheduling are crucial in improving the accuracy and reducing calculation time. In multi-dimensional simulated tempering, the first order phase transition is accessible. Therefore it is important to study the tuning of parameter set and the scheduling of exchanges in the parallel counterpart, the multi-dimensional REM. We extend Hukushima's constant exchange probability method to multi-dimensional REM for the parameter set. We further propose a combined method to use this set and the Bittner-Nussbaumer-Janke'…
Replica-exchange Wang-Landau sampling: Pushing the limits of Monte Carlo simulations in materials sciences
我们描述了使用复制交换Wang-Landau（REWL）采样的材料的热力学研究，这是一种用于大规模并行实现Wang-Landau Monte Carlo方法的通用框架。为了评估该方法的性能和可扩展性，我们使用经典的海森堡模型参数化的第一性原理计算研究体心立方（bcc）铁的磁相变。我们证明，我们的框架导致了显着的加速，而不影响的准确性和精度，并有利于研究更大的系统比它的串行对应。
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation
由于对基于温度的采样方法（如副本交换）的兴趣越来越大，本文旨在进行一些观察，并提出一些我们在文献中尚未充分解决的潜在重要问题。主要是，我们希望提请注意的限制，最大的速度从温度为基础的方法预期，也注意到需要仔细量化的采样效率。由于可能需要进行长期研究来解决这些问题，我们认为将其提请更广泛的社会关注是有益的。这里对\emph{we are strictly concerned with canonical sampling at a fixed temperature,}和\emph{not}进行构象搜索。
We demonstrate the feasibility of performing sufficient configurational sampling of disordered oxides directly from first principles without resorting to the use of fitted models such as cluster expansion. This is achieved by harnessing the power of modern-day cluster supercomputers using the replica exchange Monte Carlo method coupled directly with structural relaxation and energy calculation performed by density functional codes. The idea is applied successfully to the calculation of the temperature-dependence of the degree of inversion in the cation sublattice of MgAl$_2$O$_4$ spinel oxide.…
We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble based criterion in which the other ensembles represent an environment that might or might not participate in the Mo…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy minima. In this paper, a new method of this kind is proposed in which the well-sliced metadynamics approach (WSMTD) is united with Replica Exchange with Solute Tempering (REST2) method. WSMTD employs a divide-and-conquer strategy wherein high-dimensional slices of a free energy surface are independently sampled and combined. The method enables one to accomplish a …
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information that cannot be obtained experimentally. Replica Exchange is an enhanced sampling technique that allows converged results to be obtained faster in comparison to regular molecular dynamics simulations. In this work we report the implementation, also available with GPU-accelerated code, of pH and redox potential (E) as options for multidimensional REMD simulat…
