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.

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 simulation analysis of conessine against multi drug resistant Serratia marcescens

2019 ◽  
Vol 67 ◽  
pp. 101-111
Author(s):  
Kalyani Dhusia ◽  
Kalpana Raja ◽  
Pierre Paul Michel Thomas ◽  
Pramod K. Yadav ◽  
Pramod W. Ramteke
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Serratia Marcescens ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Drug Resistant

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.

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 simulation of the solidification process of multicrystalline silicon from homogeneous nucleation to grain coarsening

CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Homogeneous Nucleation ◽  
Solidification Process ◽  
Dynamics Simulation ◽  
Multicrystalline Silicon ◽  
Solidification Processes ◽  
Dynamics Simulations ◽  
Weber Potential

Based on the Stillinger–Weber potential, molecular dynamics simulations of the solidification processes of multicrystalline silicon were carried out.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.

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