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Tag Archives: gromacs
Molecular basis of ion translocation in sodium/proton antiporters

Molecular basis of ion translocation in sodium/proton antiporters

We studied the process of sodium/proton antiport in the NapA transporter. Through a combination of X-ray crystallography, biochemistry and computer simulations we could show that the antiporter undergoes a large conformational transition that resembles a *elevator*-like movement whereby a single domain moves up- and down through the membrane and carries a sodium ion with it.

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Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

We show that one of the best-studied secondary active transporters, the lactose permease LacY, goes through an occluded conformation during its transport cycle. We propose an atomically detailed model of the apo-occluded state. The simulations predict the formation of a transient salt bridge that has been hypothesized in the canonical model for transport of LacY. The simulations are validated by comparison to experimental EPR DEER data, using a new approach to simulate spin-label distance distributions through post-processing of molecular dynamics trajectories. We also define a set of order parameters that consistently classify all known MFS transporter structures as outward-open, occluded, or inward-open conformations.

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Tutorial: Simulating AdK with Gromacs

Tutorial: Simulating AdK with Gromacs

A tutorial that teaches you to perform and analyze a molecular dynamics simulation of the the enzyme adenylate kinase (AdK) with the Gromacs simulation package.

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PHY494/PHY598/CHM598 — Simulation approaches to Bio- and Nanophysics

PHY494/PHY598/CHM598 — Simulation approaches to Bio- and Nanophysics

The course will teach you the theoretical background on how to simulate systems at the atomic scale (e.g. using molecular dynamics), you will learn to program some of the fundamental algorithms, and you will be using state-of-the art software to run simulations of problems in areas of active research. The focus is on bio/nanophysics but there’s room to accommodate individual interests. The course will be half lecture, half hands-on work in a computer lab.

Note that this course is currently not scheduled. It ran the last time in Spring 2013.

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Molecular Dynamics Simulation of a Carbon Nanotube Gigahertz Oscillator

Molecular Dynamics Simulation of a Carbon Nanotube Gigahertz Oscillator

As part of his final project for the course Simulation Approaches to Bio- and Nanophysics (ASU PHY494/PHY598), C. Michael Gilbert performed classical molecular dynamics simulations of a smaller carbon nanotube in a larger one.

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GromacsWrapper

GromacsWrapper

GromacsWrapper is a python package that allows one to call the standard Gromacs tools in Python scripts. It is object-oriented and encourages code reuse and is therefore suitable for scripting complex work flows for setting up or analyzing Gromacs MD simulations.

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MDAnalysis

MDAnalysis

MDAnalysis is an open source, versatile, object-oriented Python library for analyzing molecular dynamics trajectories. It makes it easy to access trajectory data from Python code by interfacing trajectory readers (and writers) with NumPy arrays and to select atoms via a expressive selection syntax. The CHARMM/NAMD, Amber, Gromacs trajectory formats are all supported as well as PDB, GRO, CRD, PQR, and a range of others.

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Lipidbook

Lipidbook

Lipidbook is a public repository and database for force field parameters with a special emphasis on lipids, detergents, and similar molecules that are of interest when simulating biological membranes.

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