Difference between revisions of "CHARMM"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
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[[Category:Software]][[Category:Chemistry]]
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[[Category:Software]][[Category:Chemistry]][[Category:Simulation]]
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<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
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<!--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/"
 
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Optional variables:
 
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INTEL - Version of the Intel Compiler e.g. "11.1"
 
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MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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-->
 
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{|
 
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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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<!--Compiler and MPI settings - OPTIONAL -->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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<!--Choose sections to enable - OPTIONAL-->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
|{{#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-->
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 +
 
 
CHARMM (Chemistry at HARvard Macromolecular Mechanics):
 
CHARMM (Chemistry at HARvard Macromolecular Mechanics):
  
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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
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<!--Location-->
 
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{{App_Location|app={{#var:app}}|{{#var:ver}}}}
 
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==Available versions==
 
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===35b2===
 
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* See [[CHARMM_35b2|the 35b2 version page for more details]].
 
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===36a3===
 
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* See [[CHARMM_36a3|the 36a3 version page for more details]].
 
 
<!-- -->
 
<!-- -->
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==Running the application using modules==
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==Required Modules==
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To use charmm with the environment modules system at HPC the following commands are available:
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[[Modules|modules documentation]]
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Get module information for CHARMM:
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===Serial (GNU)===
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module spider charmm
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*{{#var:app}}
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{{#if: {{#var: mod}}|==Running the application using modules==
 
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
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In addition the CHARMM module can be loaded via a single command:
 
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module load intel/10.1 mvapich charmm
 
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{{#if: {{#var: exe}}|==How To Run==
 
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<pre>
 
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#!/bin/bash
 
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#
 
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#PBS -N ASNS-MD
 
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#PBS -o charmm.log
 
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#PBS -e charmm.err
 
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#PBS -j oe
 
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#PBS -m abe
 
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#PBS -M taylor@ufl.edu
 
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#PBS -l nodes=1:ppn=4
 
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#PBS -l pmem=900mb
 
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#PBS -l walltime=00:10:00
 
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module load intel/11.1
 
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module load openmpi/1.4.3
 
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module load charmm/36a3
 
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exeFile=/apps/charmm/35b2/exec/em64t/charmm 
 
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exeFile=/home/taylor/c36a3mpi/exec/em64t/charmm
 
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inputFile=step4.1_heat.inp
 
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outputFile=step4.1_heat.out
 
  
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echo "---------------------------------------------------------------"
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===Parallel===
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echo "mpirun    = " `which mpirun`
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*intel
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echo "charmm    = " $exeFile
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*openmpi
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echo "directory = " $PBS_O_WORKDIR
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*{{#var:app}}
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echo "---------------------------------------------------------------"
 
  
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cd $PBS_O_WORKDIR
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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rm -f charmm.inp
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* HPC_{{uc:{{#var:app}}}}_LIB - library directory
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ln -s $inputFile charmm.inp
 
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mpiexec $exeFile  > $outputFile 2>&1
 
−
</pre>|}}
 
 
{{#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 policy==
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{{#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 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




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=CHARMM&oldid=23324"