GROMACS: Fast, flexible, and free

Spoel, David van der; Lindahl, Erik; Hess, Berk; Groenhof, Gerrit; Mark, Alan E.; Berendsen, Herman J. C.

doi:10.1002/jcc.20291

Cited by 15,414 publications

(11,049 citation statements)

References 138 publications

Supporting

Mentioning

10,976

Contrasting

Unclassified

Order By: Relevance

“…All simulations were performed in the NPT ensemble with GROMACS 4.6.4 42. Covalent bonds involving hydrogens were constrained using LINCS43 while water molecules were kept rigid with SETTLE,44 allowing the use of a 2 fs time step.…”

Section: Methodsmentioning

confidence: 99%

Area Increase and Budding in Giant Vesicles Triggered by Light: Behind the Scene

et al. 2018

View full text Add to dashboard Cite

Biomembranes are constantly remodeled and in cells, these processes are controlled and modulated by an assortment of membrane proteins. Here, it is shown that such remodeling can also be induced by photoresponsive molecules. The morphological control of giant vesicles in the presence of a water‐soluble ortho‐tetrafluoroazobenzene photoswitch (F‐azo) is demonstrated and it is shown that the shape transformations are based on an increase in membrane area and generation of spontaneous curvature. The vesicles exhibit budding and the buds can be retracted by using light of a different wavelength. In the presence of F‐azo, the membrane area can increase by more than 5% as assessed from vesicle electrodeformation. To elucidate the underlying molecular mechanism and the partitioning of F‐azo in the membrane, molecular dynamics simulations are employed. Comparison with theoretically calculated shapes reveals that the budded shapes are governed by curvature elasticity, that the spontaneous curvature can be decomposed into a local and a nonlocal contribution, and that the local spontaneous curvature is about 1/(2.5 µm). The results show that exo‐ and endocytotic events can be controlled by light and that these photoinduced processes provide an attractive method to change membrane area and morphology.

show abstract

Section: Methodsmentioning

confidence: 99%

Area Increase and Budding in Giant Vesicles Triggered by Light: Behind the Scene

et al. 2018

View full text Add to dashboard Cite

show abstract

“…All MD simulations are performed using the GROMACS package (version 5.0.5). [47][48][49][50] The systems have been first equilibrated in the NVT ensemble (constant Number of particles, Volume, and Temperature) for 100 ps, subsequently NPT ensemble simulations are performed. MD production runs are performed for at least 200 ns (for some systems we performed runs up to 600 ns in order to achieve equilibrium configuration) for each interface model listed in Table 3.…”

Section: Computational Details Force Field (Ff) Molecular Dynamics Camentioning

confidence: 99%

Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles

et al. 2017

View full text Add to dashboard Cite

Nanophase segregation of a bi-component thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of inter-chain hydrogen bonds. The predicted phase segregation is experimentally confirmed by the synthesis of 35 and 15 nm gold nanoparticles functionalized with several binary mixtures of ligands. An extensive study by transmission electron microscopy and electron tomography using silica selective heterogeneous nucleation on acid-rich domains to provide electron contrast supports simulations and highlights patchy nanoparticles with a trend towards Janus nano-objects depending on the nature of the ligands and the particle size. These results validate our computational platform as an effective tool to predict nanophase separation in organic mixtures on a surface and drive further exploration of advanced nanoparticle functionalization.

show abstract

“…Here a denotes the power of the respective LJ terms (6,12). Both potential and force are continuous and smoothly decay to zero between r shift and the cut-off distance r cut (see also the discussion in ref.…”

mentioning

confidence: 99%

“…All simulations were performed with GROMACS, version 3.3.1. 6 Results are summarized in Table 1 (NVE) and Table 2 (NpT). The NVE simulations show that, indeed, energy sinks or wells are present.…”

mentioning

confidence: 99%