z The results published by Kandt, Schlitter, and Gerwert in a recent issue of Biophysical Journal (Kandt et al., 2004) on molecular dynamics (MD) simulations of bacteriorhodopsin (bR) trimer in a water/lipid environment represent a new and valuable step in the field of bacteriorhodopsin modeling and, more generally, in the developing field of simulations of fully integrated and functional membr...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machi...

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years seve...

To gain a better understanding of how monovalent salt under physiological conditions affects plasma membranes, we have performed 200 ns atomic-scale molecular dynamics simulations of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers. These two systems provide representative models for the outer and inner leaflets of the plasma membrane, respectively. The implications of ...

Abstract Molecular docking is one of the most popular computational tools for hit discovery step in drug design. However, there ample room improvement docking's ability to identify correct binding modes and discriminate active from decoy compounds. dynamics (MD) simulations protein–ligand structures have been shown be effective improving results. Here, we present CHARMM‐GUI high‐throughput simu...

ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR),...

The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around nearly two decades. Originally developed lipid-based systems by the groups of Marrink and Tieleman, model over years extended as community effort to current level general-purpose field. Apart from obvious benefit reduction in computational cost, popularity is largely due systematic yet intuitive ...

Molecular dynamic simulations of polyacrylic acid polyelectrolyte (PAA) analyzed its interaction with the main minerals that make up characteristic tailings mining industry, in this case, quartz, kaolinite, and montmorillonite. The were carried out package Gromacs 2020.3. potentials used General AMBER Force Field (GAFF) for PAA CLAYFF-MOH mineral surfaces. SPC/E model described water molecules ...

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and angles. This allows us to extend length of interval therefore range physical phenomena that afford simulate. We examine existing algorithms software for solving nonlinear constraint equations in parallel explain why it is necessary advance state-of-the-art. present ILVES-PC, a new a...