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 six 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 Wang, D., McCully, M.E., Luo, Z., McMichael, J., Tu, A., Daggett, V., Regnier, M. Structural and function consequences of cardiac tropinin C L57Q and I61Q Ca2+-desensitizing variants. Archives of Biochemistry and Biophysics , : in press, 2013. [ DOI ] Rizzuti, B., Daggett V. Using simulations to provide the framework for experimental protein folding studies. Archives of Biochemistry and Biophysics , 531: 128-135, 2013. [ DOI ] McCully M.E., Beck D.A.C., Daggett V. 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
Root Mean Square Deviation in Vacuum Root mean square deviation (RMSD) was measured for 3310 diverse molecules from the Automated Topology Builder (ATB). The Quantum Mechanics (QM) optimized structure was compared with the structure obtained after energy minimization in vacuum. The number of atoms for the molecules varied from 4 to 659. The molecular weight ranged from 17 to 4453 u. The molecules consisted of atoms such as carbon, hydrogen, oxygen, silicon, sulphur, phosphorus, nitrogen and halogens (chlorine, bromide, fluorine). 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 756 matches Re: [gmx-users] atom H is missing in the first residue in a chain 2009/01/15 Hi Justin/Zhong Zheng, Use - ignh to allow the relevant .hdb file to add the appropriate hydrogens. 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 2007 11:11 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 David van der Spoel spoel at xray.bmc.uu.se Tue Sep 17 15:00:10 CEST 2002 On Tue, 2002-09-17 at 13:22, xu yechun wrote: Dear all, I have a question about adding ions to non-zero charged system. For example, a system with 8 positive charge, Is it enough to add only 8 CL ions on the 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 Restricted rotational diffusion of rigid bodies Analytical solution to the restricted‐diffusion‐in‐a‐cone model for a symmetric top is obtained using a set of orthogonal functions of nonintegral order. It is shown that the case of the restricted‐diffusion‐in‐a‐cone model for an asymmetric top cannot be solved in analytical closed form: Series solution is, however, possible.
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 March 18, 2013 New for March 22, 2013 Chemistry Highlights from Early Edition
Papers+Conferences | Structural Bioinformatics Lab