Example JSON input file

Here’s an input file to get you started:

{
    "scheduler": "pbs",
    "HPC_job": "True",
    "pbs_settings": {
        "walltime": "72:0:0",
        "nnodes": 1,
        "ncpus": 1,
        "ngpus": 1,
        "mem":"1000mb",
        "host":"cx1-51-6-1",
        "queue":"gpgpu",
        "gpu_type":"K80"
    },
    "simulation_details": {
        "system_name": "protein1",
        "inpcrd_file": "protein1.inpcrd",
        "topology_file": "protein1.prmtop",
        "start_rst": "Heated_eq.rst",
        "input_file": "Production_cmds.in",
        "start_time": 0,
        "final_time": 500,
        "job_length": 50,
        "job_directory": "/work/username/protein1",
        "cuda_version": "7.5.18",
        "binary_location": "/path/to/AMBERHOME/bin/pmemd.cuda_SPFP",
        "pre_simulation_cmd": [
            "/path/to/AMBERHOME/bin/pmemd.cuda_SPFP -O -i premin.in -o premin.out -c ${inpcrd} -p ${prmtop} -r premin.rst -ref ${inpcrd}",
            "/path/to/AMBERHOME/bin/pmemd.cuda_SPFP -O -i sandermin1.in -o sandermin1.out -c premin.rst -p ${prmtop} -r sandermin1.rst",
            "/path/to/AMBERHOME/bin/pmemd.cuda_SPFP -O -i 02_Heat.in -o 02_Heat.out -c sandermin1.rst -p ${prmtop} -r 02_Heat.rst -ref sandermin1.rst -x 02_Heat.nc",
            "/path/to/AMBERHOME/bin/pmemd.cuda_SPFP -O -i 03_Heat2.in -o 03_Heat2.out -c 02_Heat.rst -p ${prmtop} -r Heated_eq.rst -ref 02_Heat.rst -x 03_Heat2.nc"
        ],
        "pre_simulation_type": "gpu"
    },
    "local_machine": {
        "user": "username",
        "hostname": "hostname",
        "destination" : "/Users/username/protein1"
    },
    "master_node": {
        "user_m": "username",
        "hostname_m": "master_node-hostname",
        "job_directory_m": "/home/username/protein1"
    }
}