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AMBER: Difference between revisions
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==Introduction== | ==Introduction== <!--T:1--> | ||
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. | Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. | ||
==Running Amber 16 on Graham== | ==Running Amber 16 on Graham== <!--T:2--> | ||
Amber 16 is installed on Graham and available through the modules system. You can load it using | Amber 16 is installed on Graham and available through the modules system. You can load it using | ||
[name@server $] module load amber/16 | [name@server $] module load amber/16 | ||
===Job Submission=== | ===Job Submission=== <!--T:3--> | ||
Graham uses Slurm scheduler, for details about submitting jobs, see [[Running jobs]]. | Graham uses Slurm scheduler, for details about submitting jobs, see [[Running jobs]]. | ||
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The following example is a sander serial job script, mysub.sh (inputs: in.md, crd.md.23, prmtop) | The following example is a sander serial job script, mysub.sh (inputs: in.md, crd.md.23, prmtop) | ||
#!/bin/bash | #!/bin/bash | ||
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sander -O -i in.md -c crd.md.23 -o cytosine.out | sander -O -i in.md -c crd.md.23 -o cytosine.out | ||
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The following example is a sander.MPI parallel job script, mysub.sh | The following example is a sander.MPI parallel job script, mysub.sh | ||
#!/bin/bash | #!/bin/bash | ||
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srun sander.MPI -ng 2 -groupfile groups # srun command | srun sander.MPI -ng 2 -groupfile groups # srun command | ||
<!--T:6--> | |||
You can modify the script to fit your job's requirements for compute resources. | You can modify the script to fit your job's requirements for compute resources. | ||
===Examples=== | ===Examples=== <!--T:7--> | ||
Sample *.sh and input files can be found on Graham under | Sample *.sh and input files can be found on Graham under | ||
/home/jemmyhu/tests/test_Amber/ | /home/jemmyhu/tests/test_Amber/ | ||
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