Improved GROMACS algorithms using the MPI parallelization

Goga, Nicolae; Marin, Iuliana; Vasilățeanu, Andrei; Drăgoi, George; Kadiri, K. O.; Awodele, Olufunsho

doi:10.1109/ehb.2015.7391443

Cited by 3 publications

(3 citation statements)

References 7 publications

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“…The production run was performed for 100 ns. An MD simulation with parameters such as temperature (300 K), pressure (1.0 bar), and density (1000 kg m −3 ) were stabilized over a set period (100 ns), and executed for 100 ns (i.e., time = nstep*dt, nstep = 5 crore, dt = 0.002 fs) [54][55][56]. The RMSD of the simulated and un-simulated complex were graphically plotted using the grace tool.…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach

et al. 2022

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Excitotoxicity is a type of neurodegenerative disorder. It caused by excessive glutamate receptor activation, which leads to neuronal malfunction and fatality. The N-methyl-D-aspartate (NMDA) receptors are found in glutamatergic neurons, and their excessive activation is primarily responsible for excitotoxicity. They are activated by both glutamate binding and postsynaptic depolarization, facilitating Ca2+ entry upon activation. Therefore, they are now widely acknowledged as being essential targets for excitotoxicity issues. Molecular docking and molecular dynamics (MD) simulation analyses have demonstrated that nobiletin efficiently targets the binding pocket of the NMDA receptor protein and exhibits stable dynamic behavior at the binding site. In this study, five potential neuroprotectants, nobiletin, silibinin, ononin, ginkgolide B, and epigallocatechin gallate (EGCG), were screened against the glutamate NMDA receptors in humans via computational methods. An in silico ADMET study was also performed, to predict the pharmacokinetics and toxicity profile for the expression of good drug-like behavior and a non-toxic nature. It was revealed that nobiletin fulfills the criteria for all of the drug-likeness rules (Veber, Lipinski, Ghose, Muegge, and Egan) and has neither PAINS nor structural alerts (Brenks). In conclusion, nobiletin demonstrated a possible promising neuroprotectant activities compared to other selected phytochemicals. Further, it can be evaluated in the laboratory for promising therapeutic approaches for in vitro and in vivo studies.

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Section: Molecular Dynamic Simulationmentioning

confidence: 99%

Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach

et al. 2022

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“…The multi-core systems simulation was performed upon the MARTINI coarse-grained force field developed by the molecular dynamics group from the Royal University of Groningen using a system of Martini Water [12]. The MARTINI coarse-grained force field reproduces thermodynamic properties by mapping four heavy atoms to one coarse-grained meta-particle [13,14].…”

Section: B Simulation On the Multi-core Systemsmentioning

confidence: 99%

“…The positions are updated according to the constraints. The compensation of the freedom degrees lost because of constraints is done by generating the Maxwellian velocities for all the particles (12)(13)(14).…”

Section: B Simulation On the Multi-core Systemsmentioning

confidence: 99%

Benchmarking MD systems simulations on the graphics processing unit and multi-core systems

Marin

Goga

2016

2016 IEEE International Symposium on Systems Engineering (ISSE)

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Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core systems are used as solutions to overcome this impediment. The current paper describes a comparison done between these two kinds of systems. The first system used implies the graphics processing unit, respectively CUDA with the OpenMM molecular dynamics package and OpenCL that allows the kernels to run on the GPU. This simulation is done on a new thermostat which mixes the Berendsen thermostat with the Langevin dynamics. The second comprises the molecular dynamics simulation and energy minimization package GROMACS which is based on a parallelization through MPI (Message Passing Interface) on multi-core systems. The second simulation uses another new thermostat algorithm related respectively, dissipative particle dynamics-isotropic type (DPD-ISO). Both thermostats are innovative, based on a new theory developed by us. Results show that parallelization on multi-core systems has a performance up to 33 times greater than the one performed on the graphics processing unit. In both cases temperature of the system was maintained close to the one taken as reference. For the simulation using the CUDA GPU, the faster runtime was obtained when the number of processors was equal to four, the simulation speed being 3.67 times faster compared to the case of only one processor.

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Parallelization of shortest path algorithm using OpenMP and MPI

Awari

2017

2017 International Conference on I-Smac (IoT in Social, Mobile, Analytics and Cloud) (I-Smac)

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Improved GROMACS algorithms using the MPI parallelization

Cited by 3 publications

References 7 publications

Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach

Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach

Benchmarking MD systems simulations on the graphics processing unit and multi-core systems

Parallelization of shortest path algorithm using OpenMP and MPI

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