These tutorials are designed as introductory material into using the GROMACS simulation package. GROMACS is open-source software, and has consistently been one of the fastest (if not the fastest) molecular dynamics codes available. There are currently seven tutorials available: The first is a simple system, lysozyme in water with ions. GROMACS Tutorials
Dielectric constant of distilled water .—The dielectric constant of distilled water was measured with a vacuum tube source of voltage throughout a range of periods extending from about T =1.31×10 -8 second to T =8.49×10 -8 second corresponding to vacuum wave-lengths of 3.918 meters to 25.47 meters. The value obtained for the dielectric constant is ε =78.57 at 25°C and is independent of the period within the above range of periods. Phys. Rev. 35, 613 (1930): Measurement of the Dielectric Constant and Index of Refraction of Water and Aqueous Solutions of KCl at High Frequencies
2013 | top Rysavy, S.J., Bromley, D., Daggett, V. DIVE: A graph-based visual analytics framework for big data. IEEE Computer Graphics and Application's Special Issue - BioVis , x: x, 2013, in press. [DOI] Chen, W., van der Kamp, M.W., Daggett, V. Structural and dynamic properties of the human prion protein. Daggett Group | Publications
mdp options Table of Contents
[gmx-users] Re: Extending the simulation
NMR Spectroscopy Research Group This tutorial introduces the student to the practice of Molecular Dynamics (MD) simulations of proteins. The protocol used is a suitable starting point for investigation of proteins, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information. Introduction and Outline The aim of this tutorial is to investigate differences in the conformation and dynamics of Prion Proteins (PrP) from different animal species.
NMR Spectroscopy Research Group This tutorial introduces the student to the practice of Molecular Dynamics (MD) simulations of proteins. The protocol used is a suitable starting point for investigation of proteins, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information. Introduction and Outline
Bevan Lab | Molecular Modeling at Virginia Tech
fwspidr_tutor.pdf (application/pdf Object)
Welcome to Biskit! — Biskit: python for structural bioinformatics
Automated Topology Builder Validation Statistics Automated Topology Builder version 2.0 is validated against structural and thermodynamical data. Validation against root-mean-square deviation and hydration free energies was performed. Root Mean Square Deviation In vacuum As an initial validation of the topologies and parameters generated by the ATB 2.0, each molecule was energy minimized in vacuum and the resulting structure was compared to that obtained after Quantum Mechanical (QM) optimization in implicit solvent (water) at the B3LYP/6-31G* level (≤ 50 atoms) or at the HF/STO-3G level of theory (>50 atoms) using GAMESS-US . Automated Topology Builder and Repository
GROMACS example for Pople & Salk
Table of Contents mdp options
www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ Tutorial on MD simulations using Gromacs 3.3.3 Tsjerk A. Wassenaar Outline Molecular dynamics (MD) simulations consist of three stages: First, the input data (the simulation system) has to be prepared.
1 - 10 of 796 matches Re: [gmx-users] atom H is missing in the first residue in a chain 2009/01/15 <pre>Hi Justin/Zhong Zheng, > > Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. > The problem is that, without -ignh, pdb2gmx expects all atoms (including H) > to be present in the .pdb file. ignh
User supporting list for Gromacs, Fastest Molecular Dynamics software and GPLed User supporting list for Gromacs, Fastest Molecular Dynamics software and GPLed headers Stéphane Téletchéa | 9 May 11:11 2007 Re: Very large fluctuations in dg/dl
[gmx-users] How to specify .mdp file for position restrained simulation?
[gmx-users] time constants for the Parrinello-Rahman/nose-hoover coupling
[gmx-users] about non-zero charged system
[gmx-users] Re: setting vdw cutoff with specific force-filed?
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Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models | Browse - Journal of Chemical Physics No data available. Please log in to see this content. You have no subscription access to this content. No metrics data to plot.
Table of Contents — February 15, 2012, 28 (4)
Introduction to Protein Structure, Amino Acid Sequence Analysis and Homology Modeling:: Protein Structures Guide
Telomeres and telomerase Telomeres are in the spotlight of modern biology. Whether the subject at hand is cancer, gene regulation, organismal aging, or the cloning of mammals, much seems to depend on what happens at the ends of chromosomes. Because glamorous hypotheses often persist without experimental support, it is important to ask ourselves what we really know about telomeres. This was the topic of a recent meeting entitled ‘Telomeres and telomerase: cancer, aging, and genetic instability,’ held at the Juan March Centre for International Meetings on Biology (Madrid). Leading scientists in the field of telomere biology presented their latest data in an intimate and friendly setting, as summarized below. Telomere length regulation
Selected articles appearing the week of January 20, 2014 New for January 21, 2014 Applied Physical Sciences Highlights from Early Edition
Papers+Conferences | Structural Bioinformatics Lab StructuralBioinformaticsLab Papers+Conferences Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M, Bonvin AMJJ, Cui M et al.. 2013.