cc_staff
120
edits
AMBER: Difference between revisions
Jump to navigation
Jump to search
no edit summary
(Created page with "test") |
No edit summary |
||
| Line 1: | Line 1: | ||
==Introduction== | |||
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== | |||
Amber 16 is installed on Graham and available through the modules system. You can load it using | |||
[name@server $] module load amber/16 | |||
===Job Submission=== | |||
Graham uses Slurm scheduler, for details about submitting jobs, see [[Running Jobs]]. | |||
The following example ia a sander serial job script, mysub.sh (inputs: in.md, crd.md.23, prmtop) | |||
#!/bin/bash | |||
#SBATCH --ntasks=1 # 1 cpu, serial job | |||
#SBATCH --mem-per-cpu=2G # memory per cpu | |||
#SBATCH --time=00-01:00 # time (DD-HH:MM) | |||
#SBATCH --output=cytosine.log # .log file from scheduler | |||
module load amber/16 | |||
sander -O -i in.md -c crd.md.23 -o cytosine.out | |||
The following example is a sander.MPI parallel job script, mysub.sh (inputs: in.md, crd.md.23, prmtop) | |||
#!/bin/bash | |||
#SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, MPI job | |||
#SBATCH --mem-per-cpu=2G # memory, should be less than 4G | |||
#SBATCH --time=00-01:00 # time (DD-HH:MM) | |||
#SBATCH --output=sodium.log # output .log file | |||
module load amber/16 | |||
srun sander.MPI -ng 2 -groupfile groups # srun command | |||
You can modify the script to fit your job's requirements for compute resources. | |||