VMD and NAMD

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,... Read more


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    Latest Version

    0.2.0 (Other available versions)


    Operating System

    Linux/Unix, Ubuntu Ubuntu Server 16.04 LTS


    Delivery Method

    64-bit Amazon Machine Image (AMI) (Read more)



    AWS Services Required

    Amazon EC2, Amazon EBS


    Highlights

    • Highly Scalable

    Product Description

    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. NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

    Product Details

    • Version: 0.2.0
    • Available on AWS Marketplace Since: 02/14/2017

    Resources

    Usage Instructions

    After launching the AMI, users can access the instance through the command line using SSH or visually using VNC. To connect to the instance with VNC, you will need a VNC viewer software such as the NICE DCV Endstation http://www.nice-software.com/download/nice-dcv-2016 . To access a running instance, you will need to use its public IP and port 5901 in your VNC viewer software of choice. The password is the first 8 characters of the instance id. For command line access with SSH, you should log in to the public IP with user "ubuntu" and using the keypair you selected when launching the AMI. For more information, see http://www.ks.uiuc.edu/Research/cloud/

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    Support Details

    VMD and NAMD

    Mailing lists

    http://www.ks.uiuc.edu/Research/namd/mailing_list/ http://www.ks.uiuc.edu/Research/vmd/mailing_list/

    AWS Infrastructure

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    Refund Policy

    no refunds

    End User License Agreement

    By subscribing to this product you agree to terms and conditions outlined in the product End User License Agreement (EULA).

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