scholarly journals gmxapi: a Gromacs-native Python interface for molecular dynamics with ensemble and plugin support

2021 ◽  
Author(s):  
M. Eric Irrgang ◽  
Caroline Davis ◽  
Peter Kasson
Keyword(s):  
Molecular Dynamics ◽  
Flow Simulation ◽  
Dynamics Simulation ◽  
Command Line ◽  
Level Data ◽  
Python Scripting ◽  
Multiple Levels ◽  
Dynamics Simulations ◽  
High Level ◽  
Levels Of Integration

Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is installed by default in current versions of the software. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.

HeroMDAnalysis: an automagical tool for GROMACS-based molecular dynamics simulation analysis

2021 ◽  
Vol 13 (5) ◽  
pp. 447-456
Author(s):  
Ravi Rawat ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Kajal Bhati ◽  
Saurabh M. Verma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Graphical User Interface ◽  
Simulation Analysis ◽  
Prior Experience ◽  
Dynamics Simulation ◽  
Command Line ◽  
Command Line Interface ◽  
High Quality ◽  
Dynamics Simulations

Background & objective: Molecular dynamics simulations (MDS) using GROMACS are among the commonly used computational experiments in the area of molecular biology and drug discovery. This article presents a project called HeroMDAnalysis, an automagical tool to analyze the GROMACS-based MDS trajectories and generate plots as high-quality images for various parameters. Materials & methods: The tool was built using bash shell programming, and graphical user interface was built using Zenity engine. Results & conclusion: This tool offers a simple, semiautomated, and relatively fast framework for what was previously a complex, manual, time-consuming and error-prone task, presenting a useful method for biochemists and synthetic chemists with no prior experience of the command line interface.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

2017 ◽  
Vol 890 ◽  
pp. 252-259
Author(s):  
Le Wang ◽  
Guan Cheng Jiang ◽  
Xin Lin ◽  
Xian Min Zhang ◽  
Qi Hui Jiang
Keyword(s):  
Molecular Dynamics ◽  
Water Movement ◽  
Simulation Analysis ◽  
Mass Density ◽  
Dynamics Simulation ◽  
Dissociation Process ◽  
Hydrate Dissociation ◽  
Hydrocarbon Chains ◽  
Dynamics Simulations ◽  
Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Molecular Dynamics Simulation of Sputtering with Mmany-Body Interactions

1988 ◽  
Vol 100 ◽  
Author(s):  
Davy Y. Lo ◽  
Tom A. Tombrello ◽  
Mark H. Shapiro ◽  
Don E. Harrison
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Single Crystal ◽  
Low Energy ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Many Body ◽  
Embedded Atom ◽  
Dynamics Simulations ◽  
Small Single Crystal

ABSTRACTMany-body forces obtained by the Embedded-Atom Method (EAM) [41 are incorporated into the description of low energy collisions and surface ejection processes in molecular dynamics simulations of sputtering from metal targets. Bombardments of small, single crystal Cu targets (400–500 atoms) in three different orientations ({100}, {110}, {111}) by 5 keV Ar+ ions have been simulated. The results are compared to simulations using purely pair-wise additive interactions. Significant differences in the spectra of ejected atoms are found.

scholarly journals Molecular Dynamics Simulation of Wetting Behavior: Contact Angle Dependency on Water Potential Models

2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Lukman Hakim ◽  
Irsandi Dwi Oka Kurniawan ◽  
Ellya Indahyanti ◽  
Irwansyah Putra Pradana
Keyword(s):  
Molecular Dynamics ◽  
Contact Angle ◽  
Liquid Droplet ◽  
Center Of Mass ◽  
Contact Angles ◽  
Surface Wettability ◽  
Dynamics Simulation ◽  
Potential Models ◽  
Surface Hydrophilicity ◽  
Dynamics Simulations

The underlying principle of surface wettability has obtained great attentions for the development of novel functional surfaces. Molecular dynamics simulations has been widely utilized to obtain molecular-level details of surface wettability that is commonly quantified in term of contact angle of a liquid droplet on the surface. In this work, the sensitivity of contact angle calculation at various degrees of surface hydrophilicity to the adopted potential models of water: SPC/E, TIP4P, and TIP5P, is investigated. The simulation cell consists of a water droplet on a structureless surface whose hydrophilicity is modified by introducing a scaling factor to the water-surface interaction parameter. The simulation shows that the differences in contact angle described by the potential models are systematic and become more visible with the increase of the surface hydrophilicity. An alternative method to compute a contact angle based on the height of center-of-mass of the droplet is also evaluated, and the resulting contact angles are generally larger than those determined from the liquid-gas interfacial line.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Gold Nanoclusters ◽  
Dynamics Simulation ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Positively Charged

The complexation of siRNA with positively charged gold nanoclusters has been studied using classical molecular dynamics simulations.

Molecular Dynamics Simulations on Hydrogen Adsorption in Li Doped Single Walled Carbon Nanotube

2012 ◽  
Vol 550-553 ◽  
pp. 2712-2718
Author(s):  
Li Li Wang ◽  
Yong Jian Tang ◽  
Chao Yang Wang ◽  
Jian Bo Liu
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Storage ◽  
First Principles ◽  
Alkali Metals ◽  
Hydrogen Adsorption ◽  
Dynamics Simulation ◽  
Single Wall Carbon Nanotubes ◽  
Density Analysis ◽  
Dynamics Simulations ◽  
First Principles Molecular Dynamics

This work presents a first-principles molecular dynamics study of hydrogen storage in Li doped single-wall carbon nanotubes (SWCNTs). The decomposition and adsorption between Li atom and H2 molecular are studied by bonds analysis and energy evolvement of interaction process. The modify effects of Li doped SWCNTs are studied by band structure and of states density analysis, as well as the structure transformation of SWCNTs. The enhanced hydrogen storage in Li doped SWCNTs at room temperature and common pressure is studied by first principles molecular dynamics simulation. The relationship between dope position of Li atoms and hydrogen storage also studied, and finally confirm the best dope position and provide a reference for the further research of alkali metals doped CNT.

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