Difference between revisions of "VMD"
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== Description == | == Description == | ||
''From the VMD website:'' 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. | ''From the VMD website:'' '''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 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. | ||
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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. | 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. | ||
{{AppStandardHeader|1.9|vmd}} | |||
== Running VMD on the Cluster == | == Running VMD on the Cluster == | ||
{{PleaseReadUserGuide}} | |||
=== Starting the Application === | === Starting the Application === | ||
{{X11Connection}} | |||
Once connected to CIRCE, you can open Jmol using the steps below: | |||
= | <pre style="white-space:pre-wrap; width:40%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/vmd/1.9 | ||
[user@login0 ~]$ vmd</pre> | |||
{{Documentation}} | |||
*VMD Documentation | *VMD Documentation | ||
*http://www.ks.uiuc.edu/Research/vmd/current/docs.html | *http://www.ks.uiuc.edu/Research/vmd/current/docs.html | ||
{{ReportingBugs}} | {{ReportingBugs}} |
Revision as of 18:44, 29 June 2016
Description
From the VMD website: 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.
Version
- 1.9
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
VMD requires the following module file to run:
apps/vmd/1.9
- See Modules for more information.
Running VMD on the Cluster
The VMD user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Starting the Application
Establishing a GUI connection to CIRCE/SC
To use VMD, you will need to connect to CIRCE/SC with GUI redirection, either using:
- CIRCE/SC Desktop Environment
- SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
[user@localhost ~]$ ssh -X circe.rc.usf.edu
or[user@localhost ~]$ ssh -X sc.rc.usf.edu
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
Once connected to CIRCE, you can open Jmol using the steps below:
[user@login0 ~]$ module add apps/vmd/1.9 [user@login0 ~]$ vmd
Documentation
Home Page, User Guides, and Manuals
- VMD Documentation
- http://www.ks.uiuc.edu/Research/vmd/current/docs.html
Reporting Bugs
Report bugs with VMD to the IT Help Desk: rc-help@usf.edu