Difference between revisions of "Vmd"

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|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
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|{{#vardefine:faq|1}} <!--Enable FAQ section -->
 
|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 
|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 
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*{{#var:app}}
 
*{{#var:app}}
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
 
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 
WRITE PERFORMANCE TESTING RESULTS HERE|}}
 
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
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{{#if: {{#var: faq}}|==Additional Information==
*'''Q:''' **'''A:'''|}}
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If 3D visualization is required you will need to run this software on a HWGUI partition.
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|}}
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{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows: <br/>
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The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum: <br/>
  
 
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.  
 
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.  
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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=
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* Validated 4/5/2018

Latest revision as of 18:59, 17 November 2020

Description

vmd website  

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Required Modules

modules documentation

Serial

  • vmd

System Variables

  • HPC_VMD_DIR - installation directory
  • HPC_VMD_BIN - executable directory




Additional Information

If 3D visualization is required you will need to run this software on a HWGUI partition.

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