ArticleThe Journal of chemical physics2018
Reservoir pH replica exchange.
Article in The Journal of chemical physics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins.Journal of computational biophysics and chemistry · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir.Journal of chemical theory and computation · 2023Article
- Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers.Photosynthesis research · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- Scalable Constant pH Molecular Dynamics in GROMACS.Journal of chemical theory and computation · 2022Article
- Best Practices in Constant pH MD Simulations: Accuracy and Sampling.Journal of chemical theory and computation · 2022Article
- Protein pJournal of chemical theory and computation · 2022Article
- Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.The journal of physical chemistry. B · 2022Article
- Determinants of conductance of a bacterial voltage-gated sodium channel.Biophysical journal · 2021Article
- Poor Person's pH Simulation of Membrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.Journal of chemical theory and computation · 2020Article
- Standard state free energies, not pKJournal of computer-aided molecular design · 2020Article
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Authors and funding
4 authors.
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Abstract
We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.
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