Difference between revisions of "CHARMM"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
| (31 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
| − | [[Category:Software]][[Category:Chemistry]] | + | [[Category:Software]][[Category:Chemistry]][[Category:Simulation]] |
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|charmm}} | |{{#vardefine:app|charmm}} | ||
|{{#vardefine:url|http://www.charmm.org/}} | |{{#vardefine:url|http://www.charmm.org/}} | ||
| − | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |
| − | |{{#vardefine: | ||
| − | |||
| − | |||
| − | |||
| − | |||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| Line 31: | Line 16: | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
| − | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} |
| + | |||
CHARMM (Chemistry at HARvard Macromolecular Mechanics): | CHARMM (Chemistry at HARvard Macromolecular Mechanics): | ||
| Line 40: | Line 26: | ||
* can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models | * can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models | ||
* has been ported to numerous platforms in both serial and parallel architectures | * has been ported to numerous platforms in both serial and parallel architectures | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<!-- --> | <!-- --> | ||
| − | == | + | ==Required Modules== |
| − | + | [[Modules|modules documentation]] | |
| − | + | ===Serial (GNU)=== | |
| − | + | *{{#var:app}} | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | ===Parallel=== | |
| − | + | *intel | |
| − | + | *openmpi | |
| − | + | *{{#var:app}} | |
| − | |||
| − | + | ==System Variables== | |
| − | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |
| − | + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory | |
| − | |||
| − | |||
| − | |||
{{#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.|}} | ||
| + | <!--Additional--> | ||
| + | |||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 13:51, 6 June 2022
Description
CHARMM (Chemistry at HARvard Macromolecular Mechanics):
- is a versatile and widely used molecular simulation program with broad application to many-particle systems
- has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments
- provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities
- is useful for a much broader class of many-particle systems
- can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models
- has been ported to numerous platforms in both serial and parallel architectures
Required Modules
Serial (GNU)
- charmm
Parallel
- intel
- openmpi
- charmm
System Variables
- HPC_CHARMM_DIR - installation directory
- HPC_CHARMM_LIB - library directory