نتایج جستجو برای: molecular dynamics md simulations

تعداد نتایج: 1229332  

Journal: :Journal of Biomolecular Nmr 2007
Ulrich Sternberg Raiker Witter Anne S. Ulrich

Orientational constraints obtained from solid state NMR experiments on anisotropic samples are used here in molecular dynamics (MD) simulations for determining the structure and dynamics of several different membrane-bound molecules. The new MD technique is based on the inclusion of orientation dependent pseudo-forces in the COSMOS-NMR force field. These forces drive molecular rotations and re-...

Journal: :The journal of physical chemistry. B 2008
Deniz Sezer Jack H Freed Benoît Roux

The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the f...

Journal: :CoRR 2007
Graham B. Macpherson Jason M. Reese

A new algorithm for calculating intermolecular pair forces in Molecular Dynamics (MD) simulations on a distributed parallel computer is presented. The Arbitrary Interacting Cells Algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh, which has been spatially decomposed into irregular portions for parallelisation. It is intended for ...

Journal: :The journal of physical chemistry. B 2008
Paul Maragakis Kresten Lindorff-Larsen Michael P Eastwood Ron O Dror John L Klepeis Isaiah T Arkin Morten Ø Jensen Huafeng Xu Nikola Trbovic Richard A Friesner Arthur G Palmer David E Shaw

A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dyn...

Journal: :Chemical communications 2011
Cristina Airoldi Francisco Cardona Erika Sironi Laura Colombo Mario Salmona Artur Silva Francesco Nicotra Barbara La Ferla

A small library of glyco-fused benzopyran compounds has been synthesised. Their interaction features with Aβ peptides have been characterised by using STD-NMR and trNOESY experiments. The conformational analysis of the compounds has also been carried out through molecular mechanics (MM) and molecular dynamics (MD) simulations.

2008
Marcus B. Kubitzki Bert L. de Groot Daniel Seeliger

Understanding protein function requires detailed knowledge about protein dynamics, i.e. the different conformational states the system can adopt. Despite substantial experimental progress, simulation techniques such as molecular dynamics (MD) currently provide the only routine means to obtain dynamical information at an atomic level on timescales of nanoto microseconds. Even with the current de...

Journal: :Journal of chemical theory and computation 2013
Michal Jamroz Modesto Orozco Andrzej Kolinski Sebastian Kmiecik

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cann...

2012
Manaschai Kunaseth Ken-ichi Nomura Hikmet Dursun Rajiv K. Kalia Aiichiro Nakano Priya Vashishta

Dynamic irregular applications such as molecular dynamics (MD) simulation often suffer considerable performance deterioration during execution. To address this problem, an optimal data-reordering schedule has been developed for runtime memory-access optimization of MD simulations on parallel computers. Analysis of the memory-access penalty during MD simulations shows that the performance improv...

Journal: :Current opinion in structural biology 2012
Bosco K Ho David Perahia Ashley M Buckle

Molecular dynamics (MD) simulation is an established method for studying the conformational changes that are important for protein function. Recent advances in hardware and software have allowed MD simulations over the same timescales as experiment, improving the agreement between theory and experiment to a large extent. However, running such simulations are costly, in terms of resources, stora...

2005
Takahiro Koishi Shigeru Tamaki Toshikazu Ebisuzaki

The understanding of aqueous solution properties is recognized as being important in many areas of physical chemistry and molecular biophysics. Computer simulation has become an important tool in understanding the structure and dynamics of aqueous electrolyte solutions at the atomic or molecular level. Many works of molecular dynamics (MD) simulations have been carried out to investigate hydrat...

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