Journal ArticleDOI
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
Tsjerk A. Wassenaar,Tsjerk A. Wassenaar,Helgi I. Ingólfsson,Rainer A. Böckmann,D. Peter Tieleman,Siewert J. Marrink +5 more
TLDR
A comprehensive method for building membrane containing systems, characterized by simplicity and versatility, and a survey of properties for a large range of lipids as a start of a computational lipidomics project.Abstract:
For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complemen...read more
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Journal ArticleDOI
Computational Modeling of Realistic Cell Membranes
Siewert J. Marrink,Valentina Corradi,Paulo C. T. Souza,Helgi I. Ingólfsson,D. Peter Tieleman,Mark S.P. Sansom +5 more
TL;DR: The state of the art in the field of realistic membrane simulations is reviewed and the current limitations and challenges ahead are discussed.
Journal ArticleDOI
Martini 3 : A general purpose force field for coarse-grained molecular dynamics
Paulo C. T. Souza,Paulo C. T. Souza,Riccardo Alessandri,Jonathan Barnoud,Jonathan Barnoud,Sebastian Thallmair,Sebastian Thallmair,Ignacio Faustino,Fabian Grünewald,Ilias Patmanidis,Haleh Abdizadeh,Bart M H Bruininks,Tsjerk A. Wassenaar,Peter C. Kroon,Josef Melcr,Vincent Nieto,Valentina Corradi,Hanif M. Khan,Hanif M. Khan,Jan Domański,Jan Domański,Matti Javanainen,Hector Martinez-Seara,Nathalie Reuter,Robert B. Best,Ilpo Vattulainen,Luca Monticelli,Xavier Periole,D. Peter Tieleman,Alex H. de Vries,Siewert J. Marrink +30 more
TL;DR: The coarse-grained Martini force field is widely used in biomolecular simulations as discussed by the authors, which allows accurate predictions of molecular packing and interactions in general, exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.
Journal ArticleDOI
Martini straight: Boosting performance using a shorter cutoff and GPUs
TL;DR: It is concluded that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs.
Journal ArticleDOI
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
Jumin Lee,Dhilon S. Patel,Jonas Ståhle,Sang-Jun Park,Nathan R. Kern,Seonghoon Kim,Joonseong Lee,Xi Cheng,Miguel A. Valvano,Otto Holst,Yuriy A. Knirel,Yifei Qi,Sunhwan Jo,Jeffery B. Klauda,Göran Widmalm,Wonpil Im +15 more
TL;DR: These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolIPid-/ LPS-/LOS-containing biological membrane systems.
Journal ArticleDOI
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
TL;DR: CHARMM-GUI Martini Maker is developed, which supports 82 lipid types and different flavors of the Martini force field, and is expected to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.
References
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Journal ArticleDOI
Canonical sampling through velocity rescaling
TL;DR: In this paper, the authors present a new molecular dynamics algorithm for sampling the canonical distribution, where the velocities of all the particles are rescaled by a properly chosen random factor.