ArticleThe Journal of chemical physics2022
Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.
Article in The Journal of chemical physics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Optimization of Lennard-Jones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field.The journal of physical chemistry. B · 2025Article
- Isotropic Periodic Sum for Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2025Article
- Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.Journal of chemical theory and computation · 2025Article
- TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations.Journal of chemical theory and computation · 2025Article
- Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials.Journal of chemical information and modeling · 2025Article
- Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents.Journal of chemical theory and computation · 2024Article
- Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2024Article
- Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation.Journal of medicinal chemistry · 2023Article
- AmberTools.Journal of chemical information and modeling · 2023Article
- Streamlining and Optimizing Strategies of Electrostatic Parameterization.Journal of chemical theory and computation · 2023Article
- Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.Journal of chemical theory and computation · 2023Article
- Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2023Article
- Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Our previous article has established the theory of molecular dynamics (MD) simulations for systems modeled with the polarizable Gaussian multipole (pGM) electrostatics [Wei et al., J. Chem. Phys. 153(11), 114116 (2020)]. Specifically, we proposed the covalent basis vector framework to define the permanent multipoles and derived closed-form energy and force expressions to facilitate an efficient implementation of pGM electrostatics. In this study, we move forward to derive the pGM internal stress tensor for constant pressure MD simulations with the pGM electrostatics. Three different formulations are presented for the flexible, rigid, and short-range screened systems, respectively. The analytical formulations were implemented in the SANDER program in the Amber package and were first validated with the finite-difference method for two different boxes of pGM water molecules. This is followed by a constant temperature and constant pressure MD simulation for a box of 512 pGM water molecules. Our results show that the simulation system stabilized at a physically reasonable state and maintained the balance with the externally applied pressure. In addition, several fundamental differences were observed between the pGM and classic point charge models in terms of the simulation behaviors, indicating more extensive parameterization is necessary to utilize the pGM electrostatics.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.