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Gromacs User Manual Version 4.6
E. Apol,Rossen Apostolov,Herman J. C. Berendsen,A. van Buuren,Pär Bjelkmar,R. van Drunen,A. Feenstra,S. Fritsch,Gerrit Groenhof,Christoph Junghans,Peter M. Kasson,Per Larsson,P. Meulenhoff,Teemu Murtola,Szilárd Páll,Sander Pronk,Roland Schulz,Michael R. Shirts,A Sijbers,P. Tieleman,Berk Hess,D. van der Spoel,Erik Lindahl +22 more
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The article was published on 2013-01-01 and is currently open access. It has received 132 citations till now.read more
Citations
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Journal ArticleDOI
Computer Modeling of Halogen Bonds and Other σ-Hole Interactions
TL;DR: Advances from about the last 10 years in understanding those interactions related to σ-hole are summarized, with particular attention to theoretical and computational techniques, which play a crucial role in the field.
Journal ArticleDOI
Optimization of parameters for molecular dynamics simulation using smooth particle‐mesh Ewald in GROMACS 4.5
Mark Abraham,Jill E. Gready +1 more
TL;DR: This tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade‐off between cost and scientific reliability in biomolecular applications.
Journal ArticleDOI
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
Jessica Nasica-Labouze,Massimiliano Meli,Philippe Derreumaux,Giorgio Colombo,Normand Mousseau +4 more
TL;DR: This work combines the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigates the oligomerization process of the GNNQQNY for three system sizes.
Journal ArticleDOI
Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
S. Y. Mashayak,Mara Jochum,Konstantin Koschke,Narayana R. Aluru,Victor Rühle,Christoph Junghans +5 more
TL;DR: Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization for systematic coarse-graining of SPC/E bulk water and more complex water-methanol mixture systems using the VOTCA package.
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Force-Sensitive Autoinhibition of the von Willebrand Factor Is Mediated by Interdomain Interactions
Camilo Aponte-Santamaría,Volker Huck,Sandra Posch,Agnieszka K. Bronowska,Sandra Grässle,Maria A. Brehm,Tobias Obser,Reinhard Schneppenheim,Peter Hinterdorfer,Stefan W. Schneider,Carsten Baldauf,Frauke Gräter +11 more
TL;DR: In this article, a force-sensory mechanism for van Willebrand factor-platelet binding was proposed based on a combination of molecular dynamics simulations, atomic force microscopy (AFM), and microfluidic experiments.
References
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Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
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Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
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Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
Stuart Geman,Donald Geman +1 more
TL;DR: The analogy between images and statistical mechanics systems is made and the analogous operation under the posterior distribution yields the maximum a posteriori (MAP) estimate of the image given the degraded observations, creating a highly parallel ``relaxation'' algorithm for MAP estimation.
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Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.