VMD
From HP-SEE Wiki
Contents |
- Web site: http://www.ks.uiuc.edu/Research/vmd/
- Described version: xx.xx
- Licensing: Non-Exclusive, Non-Commercial Use License
- User documentation: link
- Download: link
- Source code: link
Authors/Maintainers
- Also origin, if the software comes from a specific project.
Summary
VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. Modern graphics processing units (GPUs) contain hundreds of arithmetic units and can be harnessed to provide tremendous acceleration for many numerically intensive scientific applications. Beginning with version 1.8.7, VMD supports CUDA for GPU acceleration of electrostatic potential map calculations, for implicit ligand sampling, and for display of molecular orbitals for quantum chemistry visualization.
Features
- Listed features
Architectural/Functional Overview
- high level design info, how it works, performance - may be a link, or several links
Usage Overview
- If possible with small example - may be a link
Dependacies
- list of all relevant dependencies on other libraries
HP-SEE Applications
- IsyMAB
Resource Centers
- IFIN_Bio, RO
- BG, BG
- HPCG, BG
- NCIT-Cluster, RO
Usage by Other Projects and Communities
- If any
Recommendations for Configuration and Usage
Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.
Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:
- Common configuration settings of execution environment
- Filesystem path or local access string
- Environment variables to be set or used by applications
- Options (e.g. additional modules) that are needed or required by applications and should be present
- Minimum quantitative values (e.g. quotas) offered by the site
- Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy
- Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins
- Conventions for application or job bound installation and usage of the resource
