The properties of sodium dodecyl sulfate (SDS) aggregates were studied through extensive molecular dynamics simulations with explicit solvent. First, we provide a parametrization of the model within Gromacs. Then, we probe the kinetics of aggregation by starting from a random solution of SDS molecules and letting the system explore its kinetic pathway during the aggregation of multiple units. W...

Summary: The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visual...

The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to microseconds time scales or faster can be studied directly. Unfortunately, apart from a few exceptions, relevant processes, such as chemical reactions or many large scale conformational transitions in proteins, occur at slo...

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Gener...

Silicon carbide nanotube (SiCNT) come forward in the great variety of nanotubes with higher durability until 1600 oC (in air) while carbon can stay stable 600 air). First five buckling loads single SiCNT placed between source and drain metal electrodes nano sized field effect transistors (FET) is investigated using two different molecular dynamics methods. L.A.M.M.P.S. software Gromacs package ...

Objective: The purpose of this study was to determine the structural-based molecular interactions between flavonoids contained in Acalypha indica L. and caspase-3 by docking dynamics (MD) simulations.
 Methods: In a computer simulation, ten A. were evaluated for using X-ray crystal structure human (PDB ID 1NME). AutoDock 4.2 software used docking, MD simulations done with GROMACS v2018.&#x...

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncert...

Motivation: Molecular dynamic simulations of membrane systems are an important method for the prediction and analysis of physicochemical properties. The CELLmicrocosmos 2.2 MembraneEditor (CmME) provides a comfortable workflow to generate lipid membranes with different conformations. While CmME is intended to generate molecular structures on desktop and mobile computers in a very short time, th...

GROMACS is one of the most widely used HPC software packages using Molecular Dynamics (MD) simulation technique. In this work, we quantify parallel performance different configurations, systems, and FFT libraries (FFTW, Intel MKL FFT, PACK). We break down cost each computational phase identify non-scalable stages, such as MPI communication during 3D computation when a large number processes. sh...