Difference between revisions of "CHARMM"
| Line 51: | Line 51: | ||
module load intel/10.1 mvapich charmm | module load intel/10.1 mvapich charmm | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | <pre> | |
| + | #!/bin/bash | ||
| + | # | ||
| + | #PBS -N ASNS-MD | ||
| + | #PBS -o charmm.log | ||
| + | #PBS -e charmm.err | ||
| + | #PBS -j oe | ||
| + | #PBS -m abe | ||
| + | #PBS -M taylor@ufl.edu | ||
| + | #PBS -l nodes=1:ppn=4 | ||
| + | #PBS -l pmem=900mb | ||
| + | #PBS -l walltime=00:10:00 | ||
| + | |||
| + | module load intel/11.1 | ||
| + | module load openmpi/1.4.3 | ||
| + | module load charmm/36a3 | ||
| + | |||
| + | exeFile=/apps/charmm/35b2/exec/em64t/charmm | ||
| + | exeFile=/home/taylor/c36a3mpi/exec/em64t/charmm | ||
| + | inputFile=step4.1_heat.inp | ||
| + | outputFile=step4.1_heat.out | ||
| + | |||
| + | echo "---------------------------------------------------------------" | ||
| + | echo "mpirun = " `which mpirun` | ||
| + | echo "charmm = " $exeFile | ||
| + | echo "directory = " $PBS_O_WORKDIR | ||
| + | echo "---------------------------------------------------------------" | ||
| + | |||
| + | cd $PBS_O_WORKDIR | ||
| + | |||
| + | rm -f charmm.inp | ||
| + | ln -s $inputFile charmm.inp | ||
| + | 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.|}} | ||
Revision as of 18:23, 30 April 2012
Description
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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
Available versions
35b2
Running the application using modules
To use charmm with the environment modules system at HPC the following commands are available:
Get module information for charmm:
$module spider charmm
Load Intel compiler:
$module load intel/10.1
Load MPI implementation:
$module load mvapich
Load the default application module:
$module load charmm
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CHARMM_DIR - directory where charmm is located.
In addition the CHARMM module can be loaded via a single command:
module load intel/10.1 mvapich charmm
36a3
| | |
Running the application using modules
To use charmm with the environment modules system at HPC the following commands are available:
Get module information for charmm:
$module spider charmm
Load Intel compiler:
$module load intel/11.1
Load MPI implementation:
$module load openmpi/1.4.3
Load the default application module:
$module load charmm
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CHARMM_DIR - directory where charmm is located.
In addition the CHARMM module can be loaded via a single command:
module load intel/11.1 openmpi/1.4.3 charmm
How To Run
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY