VMD - Visual Molecular Dynamics. Free Energy Method Tutorials. VMD Installation Guide. Tutorials. Tutorial-l Mailing List. Axel Kohlmeyer. As with any home page of any person that has a busy life, these pages are only occasionally updated and thus are constantly on the verge of becoming obsolete.
The main purpose for keeping these pages around is to have a location to conveniently make material available that i have been working on, without being subjected to the constant file layout changes of university run webpages and without being tied to my current employer. My current position is that of a Associate Dean for Scientific Computing in the College of Science and Technology as well as Associate Director of the Institute for Computational Molecular Science and Assistant Vice President for High-Performance Computing, all at Temple University in Philadelphia, PA. On E-mails: As you may expect, I get a lot of e-mails, so I kindly ask you to understand that I am not always able to answer any question that is posed to me and that my replies may be delayed, short, and blunt.
Plugins. In addition to Tcl and Python scripts, VMD implements "plugin" interfaces which provide a means for extending VMD at run-time without the necessity to recompile the program.
The two primary types of plugins for VMD are 'molfile' plugins for reading and writing data files containing atomic, graphics, and volumetric data, and scripting extensions which implement new commands and user interfaces for performing tasks such as structure building, simulation setup, etc. This page contains plugins which can be downloaded and installed in your copy of VMD, as well as any pertinent documentation that goes along with the plugins. License The VMD plugins are provided under the UIUC Open Source License, any exceptions are explicitly marked as such.
Plugin Developer Documentation: Plugin Programmer's Guide — describes the VMD plugin architecture so others can develop and build new plugins, and to use the VMD plugins in other software. Acemd. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale - Journal of Chemical Theory and Computation. Information and Communications Technologies, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom, Department de Fisica Fundamental, Universitat de Barcelona, Carrer Marti i Franques 1, 08028 Barcelona, Spain, and Computational Biochemistry and Biophysics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain J.
Chem. Theory Comput., 2009, 5 (6), pp 1632–1639 DOI: 10.1021/ct9000685 Publication Date (Web): May 21, 2009 Copyright © 2009 American Chemical Society Section: Abstract The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. Citing Articles View all 32 citing articles Citation data is made available by participants in CrossRef's Cited-by Linking service. This article has been cited by 32 ACS Journal articles (5 most recent appear below). ACEMD Forum. Gtc-express-acemd-webinar. Acellera. ACEMD. ACEMD is a production bio-molecular dynamics (MD) software specially optimized to run on graphics processing units (GPUs) on NVIDIA graphics cards.
ACEMD is the world’s fastest MD engine for a single workstation and can read the popular CHARMM and AMBER force field formats. Use it Free Download ACEMD Basic to run on a single GPU. Download Versions and Pricing Find out how to unlock the full potential of ACEMD. Learn More Distinctive Features Run in the Cloud ACEMD gives you direct access to AceCloud, our Metrocubo-based cloud-computing service.
Fast ACEMD is the fastest MD engine for GPUs in the world. Robust ACEMD is the computational engine behind one of the largest distributed computing project worldwide GPUGRID.net where thousands of MD simulations are run daily. Compatible ACEMD reads CHARMM and AMBER force field input formats making it readily compatible with any NAMD or AMBER system setups. Expandable Expand ACEMD possibilities through its plug-in interface. ABINIT. The Amber Molecular Dynamics Package. BigDFT.
CASTEP. DFTB+ The Elk FP-LAPW Code. Elk CECAM Tutorial. Gaussian. Gromacs. NWChem. OpenMX. SIESTA web page. [About] [Access to the code] [Documentation] [Databases (Pseudos and Bases)] [The Team] News SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems.
A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods. The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines. USPEX. The VASP site. Vasp.