Difference between revisions of "CHARMM"
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Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
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[[Category:Software]][[Category:Chemistry]] | [[Category:Software]][[Category:Chemistry]] | ||
| − | + | {|<!--Main settings - REQUIRED--> | |
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| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|charmm}} | |{{#vardefine:app|charmm}} | ||
|{{#vardefine:url|http://www.charmm.org/}} | |{{#vardefine:url|http://www.charmm.org/}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|1}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|1}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| − | {{#if: {{#var: exe}}|== | + | ==System Variables== |
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
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Note that the parallel version of CHARMM seems to not accept input redirection and looked for "charmm.inp" even after placing "-i my_input.inp" on the command line. This is the reason for the symlink of "charmm.inp" to the actual input file in the [[CHARMM_PBS|sample script]]. | Note that the parallel version of CHARMM seems to not accept input redirection and looked for "charmm.inp" even after placing "-i my_input.inp" on the command line. This is the reason for the symlink of "charmm.inp" to the actual input file in the [[CHARMM_PBS|sample script]]. | ||
|}} | |}} | ||
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{{#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.|}} | ||
Revision as of 18:03, 10 August 2012
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
Variants
Required Modules
Serial
- charmm
System Variables
- HPC_{{#uppercase:charmm}}_DIR - installation directory
Configuration
See the CHARMM_Configuration page for charmm configuration details.
Additional Information
Note that the parallel version of CHARMM seems to not accept input redirection and looked for "charmm.inp" even after placing "-i my_input.inp" on the command line. This is the reason for the symlink of "charmm.inp" to the actual input file in the sample script.
PBS Script Examples
See the CHARMM_PBS page for charmm PBS script examples.