Difference between revisions of "CHARMM"

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m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}")
 
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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Chemistry]]
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[[Category:Software]][[Category:Chemistry]][[Category:Simulation]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|charmm}}
 
|{{#vardefine:app|charmm}}
 
|{{#vardefine:url|http://www.charmm.org/}}
 
|{{#vardefine:url|http://www.charmm.org/}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#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-->
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|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|1}} <!--Enable PBS script wiki page link-->
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|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:policy|}} <!--Enable policy section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
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* 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
==Variants==
 
* [[CHARMM_35b2|CHARMM 35b2]]
 
* [[CHARMM_36a3|CHARMM 36a3]]
 
 
<!-- -->
 
<!-- -->
 
==Required Modules==
 
==Required Modules==
 
[[Modules|modules documentation]]
 
[[Modules|modules documentation]]
===Serial===
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===Serial (GNU)===
 
*{{#var:app}}
 
*{{#var:app}}
{{#if: {{#var: exe}}|==How To Run==
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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]].
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===Parallel===
|}}
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*intel
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*openmpi
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*{{#var:app}}
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* 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.|}}
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<!--Additional-->
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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.|}}

Latest revision as of 13:51, 6 June 2022

Description

charmm website  

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

modules documentation

Serial (GNU)

  • charmm

Parallel

  • intel
  • openmpi
  • charmm

System Variables

  • HPC_CHARMM_DIR - installation directory
  • HPC_CHARMM_LIB - library directory