scholarly journals Saving Significant Amount of Time in MD Simulations by Using an Implicit Solvent Model and Elevated Temperatures

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ifat Shub ◽  
Ehud Schreiber ◽  
Yossef Kliger
Keyword(s):  
Elevated Temperatures ◽  
Md Simulations ◽  
Implicit Solvent ◽  
Dynamic Simulations ◽  
Implicit Solvent Model ◽  
Solvent Models ◽  
Solvent Model ◽  
Wide Range ◽  
Implicit Solvent Models ◽  
Computer Power

Molecular dynamic simulations are used for investigating various aspects of biological processes. Such simulations often require intensive computer power; therefore several solutions were developed to minimize the computer power needed, including the usage of elevated temperatures. Yet, such simulations are still not commonly used by the wide scientific community of chemists and biochemists. For about two years now, the molecular simulations suite GROMACS enables conducting simulations using implicit solvent models to further decrease runtimes. In order to quantify the saving in computer power, and to confirm the validity of the models, we followed the simple dissolution process of a single NaCl molecule. The results reveal approximately 350-fold decrease in real-world runtime when using an implicit solvent model and an elevated temperature, compared to using explicit water molecules and simulating at room temperature. In addition, in a wide range of temperatures, the dissolution times of NaCl are distributed, as expected, exponentially, both in explicit and in implicit solvent models, hence confirming the validity of the simulation approach. Hopefully, our findings will encourage many scientists to take advantage of the recent progress in the molecular dynamics field for various applications.

scholarly journals Predicting Octanol–Water Partition Coefficients of Fluorinated Drug-Like Molecules: A Combined Experimental and Theoretical Study

2020 ◽  
Vol 73 (8) ◽  
pp. 677
Author(s):  
Ying Min Wu ◽  
Yuvixza Lizarme Salas ◽  
Yun Cheuk Leung ◽  
Luke Hunter ◽  
Junming Ho
Keyword(s):  
Partition Coefficients ◽  
Theoretical Study ◽  
Log P ◽  
Implicit Solvent ◽  
Mean Absolute Deviation ◽  
Empirical Methods ◽  
Absolute Deviation ◽  
Solvent Models ◽  
Solvent Model ◽  
Implicit Solvent Models

In this paper, a dataset of 11 fluorinated compounds containing a variety of functional groups (amides, esters, indoles, and ethers) as well as mono, gem-difluoro, erythro-difluoro, and threo-difluoro patterns were synthesised and their octanol–water partition coefficients (log P) were measured using a shake-flask method. The resulting data was used to assess the performance of several popular empirical fragment-based methods as well as quantum chemical implicit solvent models (SMD and SM12). Overall, the empirical miLOGP, ALOGPS, and ALOGP methods performed the best with a mean absolute deviation (MAD) of ~0.25 log units, while the best performing implicit solvent model SMD has a slightly higher MAD of 0.36 log units. Based on the present work and previous studies, the miLOGP and ALOGP empirical methods are recommended for fast and moderately accurate prediction of log P for neutral organic solutes.

scholarly journals Short solvent model for ion correlations and hydrophobic association

2020 ◽  
Vol 117 (3) ◽  
pp. 1293-1302 ◽  
Author(s):  
Ang Gao ◽  
Richard C. Remsing ◽  
John D. Weeks
Keyword(s):  
Computer Simulations ◽  
Potential Of Mean Force ◽  
Implicit Solvent ◽  
Coulomb Interactions ◽  
Solvent Models ◽  
Solvent Model ◽  
Dilute Aqueous Solutions ◽  
Hydrophobic Solutes ◽  
Local Molecular Field Theory ◽  
Implicit Solvent Models

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent–solvent and solute–solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

scholarly journals Explicit and implicit modeling of nanobubbles in hydrophobic confinement

2010 ◽  
Vol 82 (1) ◽  
pp. 3-12 ◽  
Author(s):  
Joachim Dzubiella
Keyword(s):  
Large Scale ◽  
Md Simulations ◽  
Energy Functional ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Nanofluidic Devices ◽  
Capillary Evaporation ◽  
Hydrophobic Solutes

Water at normal conditions is a fluid thermodynamically close to the liquid-vapor phase coexistence and features a large surface tension. This combination can lead to interesting capillary phenomena on microscopic scales. Explicit water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capillary evaporation on nanometer scales, i.e., the formation of nanometer-sized vapor bubbles (nanobubbles) between confining hydrophobic surfaces. This phenomenon has been exemplified for solutes with varying complexity, e.g., paraffin plates, coarse-grained homopolymers, biological and solid-state channels, and atomistically resolved proteins. It has been argued that nanobubbles strongly impact interactions in nanofluidic devices, translocation processes, and even in protein stability, function, and folding. As large-scale MD simulations are computationally expensive, the efficient multiscale modeling of nanobubbles and the prediction of their stability poses a formidable task to the'nanophysical' community. Recently, we have presented a conceptually novel and versatile implicit solvent model, namely, the variational implicit solvent model (VISM), which is based on a geometric energy functional. As reviewed here, first solvation studies of simple hydrophobic solutes using VISM coupled with the numerical level-set scheme show promising results, and, in particular, capture nanobubble formation and its subtle competition to local energetic potentials in hydrophobic confinement.

scholarly journals Generalized Born Implicit Solvent Models for Biomolecules

2019 ◽  
Vol 48 (1) ◽  
pp. 275-296 ◽  
Author(s):  
Alexey V. Onufriev ◽  
David A. Case
Keyword(s):  
Md Simulations ◽  
Implicit Solvent ◽  
Molecular Mechanics Calculations ◽  
Generalized Born ◽  
Solvent Models ◽  
Explicit Consideration ◽  
Aqueous Solvation ◽  
Solvent Molecules ◽  
The Individual ◽  
Implicit Solvent Models

It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.

VERIFICATION OF THE GENERALIZED BORN MODEL AT SHORT DISTANCES

2013 ◽  
Vol 13 (06) ◽  
pp. 1340020
Author(s):  
XIAOCHUAN TANG ◽  
YONG DUAN
Keyword(s):  
Analytical Solutions ◽  
Md Simulations ◽  
Solvation Energy ◽  
Implicit Solvent ◽  
Generalized Born ◽  
Simple Description ◽  
Born Model ◽  
Solvent Models ◽  
Potential Methods ◽  
Gb Model

The generalized Born (GB) model, one of the implicit solvent models, is widely applied in molecular dynamics (MD) simulations as a simple description of the solvation effect. In the GB model, an empirical function called the Still's formula, with the algorithmic simplicity, is utilized to calculate the solvation energy due to the polarization, termed as ΔG pol . Applications of the GB model have exhibited reasonable accuracy and high computational efficiency. However, there is still room for improvements. Most of the attempts to improve the GB model focus on optimizing effective Born radii. Contrarily, limited researches have been performed to improve the feasibility of the Still's formula. In this paper, analytical methods was applied to investigate the validity of the Still's formula at short distance. Taking advantage of the toroidal coordinates and Mehler–Fock transform, the analytical solutions of the GB model at short distances was derived explicitly for the first time. Additionally, the solvation energy was numerically computed using proper algorithms based on the analytical solutions and compared with ΔG pol calculated in the GB model. With the analysis on the deficiencies of the Still's formula at short distances, potential methods to improve the validity of the GB model were discussed.

scholarly journals The validation of quantum chemical lipophilicity prediction of alcohols

2016 ◽  
Vol 9 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Martin Michalík ◽  
Vladimír Lukeš
Keyword(s):  
Linear Correlation ◽  
Quantum Chemical ◽  
Partition Coefficients ◽  
The Other ◽  
Basis Set ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Lipophilicity Prediction ◽  
Triple Zeta ◽  
Implicit Solvent Models

AbstractThe validation of octanol-water partition coefficients (logP) quantum chemical calculations is presented for 27 alkane alcohols. The chemical accuracy of predicted logPvalues was estimated for six DFT functionals (B3LYP, PBE0, M06-2X, ωB97X-D, B97-D3, M11) and three implicit solvent models. Triple-zeta basis set 6-311++G(d,p) was employed. The best linear correlation with the experimental logPvalues was achieved for the B3LYP and B97-D3 functionals combined with the SMD model. On the other hand, no linearity was found when IEF-PCM or C-PCM implicit models were employed.

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