Difference between revisions of "VMD"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| − | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | |
| + | |||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| − | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} |
| − | |}} | + | {{#if: {{#var: pbs}}|==PBS Script Examples== |
| − | + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | |
| − | {{#if: {{#var: | + | {{#if: {{#var: policy}}|==Usage Policy== |
| − | + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | |
| − | + | {{#if: {{#var: testing}}|==Performance== | |
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==Additional Information== | ||
| + | If 3D visualization is required you will need to run this software on a HWGUI partition. | ||
|}} | |}} | ||
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| − | + | {{#if: {{#var: citation}}|==Citation== | |
| − | + | The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum: <br/> | |
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| − | {{#if: {{#var: | ||
| − | + | Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. | |
| − | + | For more information, visit the official [http://www.ks.uiuc.edu/Research/vmd/allversions/cite.html How to Cite VMD webpage]. | |
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|}} | |}} | ||
| − | + | =Validation= | |
| − | + | * Validated 4/5/2018 | |
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Revision as of 19:54, 27 May 2022
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.
Environment Modules
Run module spider vmd to find out what environment modules are available for this application.
System Variables
- HPC_VMD_DIR - installation directory
- HPC_VMD_BIN - executable directory
How To Run
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY
Citation
The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum:
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
For more information, visit the official How to Cite VMD webpage.
Validation
- Validated 4/5/2018