Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations

Reißer, Sabine; Poger, David; Stroet, Martin; Mark, Alan E.

doi:10.1021/acs.jctc.7b00178

Cited by 48 publications

(80 citation statements)

References 47 publications

(91 reference statements)

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“…Previous work with the GROMOS force field used a twin-range cutoff scheme but its association with the current implementation of the integrator in GROMACS leads to artefacts in the collective properties of a lipid bilayer. 74 Despite some loss in computational efficiency, using a single-range cutoff scheme was found to counterbalance those artefacts. 74 To correct for the truncation of electrostatic interactions beyond 1.4 nm a reactionfield correction 75 with a relative dielectric constant (e r ) of 62 was applied.…”

Section: Simulation Parametersmentioning

confidence: 99%

“…74 Despite some loss in computational efficiency, using a single-range cutoff scheme was found to counterbalance those artefacts. 74 To correct for the truncation of electrostatic interactions beyond 1.4 nm a reactionfield correction 75 with a relative dielectric constant (e r ) of 62 was applied. The systems with 0.04 and 0.4 M [H 3 O + ] were simulated in triplicate and the reference system without H 3 O + ions was simulated in duplicate, each time using randomly assigned starting velocities.…”

Section: Simulation Parametersmentioning

confidence: 99%

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The effect of hydronium ions on the structure of phospholipid membranes

Deplazes

Poger

Cornell

et al. 2018

Phys. Chem. Chem. Phys.

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This work seeks to identify the mechanisms by which hydronium ions (HO) modulate the structure of phospholipid bilayers by studying the interactions of HO with phospholipids at the molecular level. For this, we carried out multiple microsecond-long unrestrained molecular dynamics (MD) simulations of a POPC bilayer at different HO concentrations. The results show that HO accumulates at the membrane surface where it displaces water and forms strong and long-lived hydrogen bonds with the phosphate and carbonyl oxygens in phospholipids. This results in a concentration-dependent reduction of the area per lipid and an increase in bilayer thickness. This study provides an important molecular-level insight into the mechanism of how HO modulates the structure of biological membranes and is a critical step towards a better understanding of the effect of low pH on mammalian and bacterial membranes.

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Section: Simulation Parametersmentioning

confidence: 99%

Section: Simulation Parametersmentioning

confidence: 99%

The effect of hydronium ions on the structure of phospholipid membranes

Deplazes

Poger

Cornell

et al. 2018

Phys. Chem. Chem. Phys.

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“…charge group, reaction-field and twin-cutoff schemes). 55,56 The latest version of GROMACS (v.2016) 57 replaced the leapfrog algorithm by a variation of the Verlet-I/r-RESPA as the multiple-step alternative method to separately integrate fast-from slow-evolving interactions. The advantage of the new Verlet method 57 is its time-reversibility and symplecticity, but at the cost of great dependency of the update frequency on the nature of the system.…”

Section: Introductionmentioning

confidence: 99%

Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes

Lima

Nader

Santos

et al. 2019

J. Braz. Chem. Soc.

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Recent developments of GROMACS v.2016 ceased to support methodological approaches used in the development and validation of the GROMOS force field. We investigated the performance of a previously developed extension of the GROMOS force field for lipopolysaccharides to reproduce the structural dynamics of bacterial outer membrane (OM) using a single cutoff for nonbonded interactions and atom-based charge truncation. We further compared this setup for use with reaction field (RF) or particle mesh Ewald (PME) approximations in the presence of simple point charge (SPC) and extended simple point charge (SPC/E) water models. We find that the OM structural dynamics is well conserved in all simulated conditions, reproducing the available experimental data within the measurement uncertainty. The SPC/E model induces a small increase in OM fluidity, and when combined with the RF correction, shows a decrease in water orientation at the membrane surface. The present simulations support the compatibility of the GROMOS-derived lipopolysaccharide (LPS) parameters for use with single cutoff and atom-based charge schemes, either with RF or PME approximations, in GROMACS v.2016. Both SPC and SPC/E water models are suitable for use, but usage of SPC/E combined with the reaction field correction needs to be further investigated.

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“…There are examples of changes assumed to be without effect on the results of MD simulations turning out to be important in the end (e.g. Reißer et al (2017)). The hypothesis that AMBER's dependence on unphysical details of the system description has no practical importance would have to be validated for all possible applications of the force field.…”

Section: Motivationmentioning

confidence: 99%

Peer Review #2 of "Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface (v0.2)"

2018

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Most of today's scientific research relies on computers and software for processing scientific information. Examples of such computer-aided research are the analysis of experimental data or the simulation of phenomena based on theoretical models. With the rapid increase of computational power, scientific software has integrated more and more complex scientific knowledge in a black-box fashion. As a consequence, its users do not know, and do not even have a chance of finding out, which assumptions and approximations their computations are based on. This black-box nature of scientific software has made the verification of much computer-aided research close to impossible.The present work starts with an analysis of this situation from the point of view of humancomputer interaction in scientific research. It identifies the key role of digital scientific notations at the human-computer interface, reviews the most popular ones in use today, and describes a proof-of-concept implementation of Leibniz, a language designed as a verifiable digital scientific notation for models formulated as mathematical equations. Most of todays scientific research relies on computers and software for processing scientific information. Examples of such computer-aided research are the analysis of experimental data or the simulation of phenomena based on theoretical models. With the rapid increase of computational power, scientific software has integrated more and more complex scientific knowledge in a black-box fashion. As a consequence, its users do not know, and do not even have a chance of finding out, which assumptions and approximations their computations are based on. This black-box nature of scientific software has made the verification of much computer-aided research close to impossible. The present work starts with an analysis of this situation from the point of view of human-computer interaction in scientific research. It identifies the key role of digital scientific notations at the human-computer interface, reviews the most popular ones in use today, and describes a proof-of-concept implementation of Leibniz, a language designed as a verifiable digital scientific notation for models formulated as mathematical equations.

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Real Cost of Speed: The Effect of a Time-Saving Multiple-Time-Stepping Algorithm on the Accuracy of Molecular Dynamics Simulations

Cited by 48 publications

References 47 publications

The effect of hydronium ions on the structure of phospholipid membranes

The effect of hydronium ions on the structure of phospholipid membranes

Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes

Peer Review #2 of "Verifiability in computer-aided research: the role of digital scientific notations at the human-computer interface (v0.2)"

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