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AMBER: Difference between revisions
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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 | ==Running Amber 16== <!--T:2--> | ||
Amber 16 is installed on Graham | Amber 16 is currently installed only on [[Graham]] due to license restrictions. Load it using the [[Using modules|module]] command: | ||
[name@server $] module load amber/16 | [name@server $] module load amber/16 | ||
===Job | ===Job submission=== <!--T:3--> | ||
For a general discussion about submitting jobs, see [[Running jobs]]. | |||
<!--T:4--> | <!--T:4--> | ||
The following example is a sander serial job script | The following example is a sander serial job script. The input files are <code>in.md, crd.md.23, prmtop</code>. | ||
{{File | {{File | ||
|name= | |name=amber_serial.sh | ||
|lang="bash" | |lang="bash" | ||
|contents= | |contents= | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --ntasks=1 | #SBATCH --ntasks=1 # 1 cpu, serial job | ||
#SBATCH --mem-per-cpu=2G | #SBATCH --mem-per-cpu=2G # memory per cpu | ||
#SBATCH --time=00-01:00 # time (DD-HH:MM) | #SBATCH --time=00-01:00 # time (DD-HH:MM) | ||
#SBATCH --output=cytosine.log # .log file from scheduler | #SBATCH --output=cytosine.log # .log file from scheduler | ||
| Line 28: | Line 28: | ||
<!--T:5--> | <!--T:5--> | ||
The following example is a sander.MPI parallel job script | The following example is a sander.MPI parallel job script: | ||
{{File | {{File | ||
|name= | |name=amber_parallel.sh | ||
|lang="bash" | |lang="bash" | ||
|contents= | |contents= | ||
| Line 39: | Line 39: | ||
#SBATCH --output=sodium.log # output .log file | #SBATCH --output=sodium.log # output .log file | ||
module load amber/16 | module load amber/16 | ||
srun sander.MPI -ng 2 -groupfile groups | srun sander.MPI -ng 2 -groupfile groups | ||
}} | }} | ||
<!--T:6--> | <!--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. See [[Running jobs]]. | ||
===Examples=== <!--T:7--> | ===Examples=== <!--T:7--> | ||