config.template.json

{
    "ligand_forcefield": "gaff2",
    "protein_forcefield": "ff14SB",
    "ligand_box_size": 15.0,
    "complex_box_size": 12.0,
    "resize": 0.75,
    "cuda": true,
    "serial_execute": "pmemd.cuda",
    "mpi_execute": "pmemd.cuda.MPI",
    "protocol": "unified",
    "remd": true,
    "np": 25,
    "ng": 25,
    "prep": {
        "temp": 300,
        "timask1": ":LIG",
        "timask2": ":MOD",
        "scmask1": ":LIG@O2,H12",
        "scmask2": ":MOD@F1",
        "em": {
            "maxcyc": 2000,
            "resstraint_wt": 5.0
        },
        "heat": {
            "nsteps": 50000,
            "resstraint_wt": 5.0,
            "ofreq": 5000
        },
        "pressurize_res": {
            "nsteps": 100000,
            "resstraint_wt": 5.0,
            "ofreq": 10000
        }
    },
    "TI": {
        "temp": 300,
        "em": {
            "maxcyc": 5000,
            "resstraint_wt": 5.0
        },
        "heat": {
            "nsteps": 50000,
            "resstraint_wt": 5.0,
            "ofreq": 5000
        },
        "pressurize_res": {
            "nsteps": 100000,
            "resstraint_wt": 5.0,
            "ofreq": 30000
        },
        "pressurize": {
            "nsteps": 500000,
            "ofreq": 50000
        },
        "production": {
            "nsteps": 1000,
            "numexchg": 2500,
            "resstraint_wt": 5.0,
            "ntwe": 0,
            "ntwx": 1000,
            "ntwr": 50000,
            "ntpr": 1000
        }
    },
    
    "unified": {
        "lambdas": [
            0.00000000, 0.17683400, 0.22976400, 0.26937900, 0.30269700, 0.33229000, 0.35943600, 0.38488600, 0.40913000,
            0.43251800, 0.45531800, 0.47774800, 0.50000000, 0.52225200, 0.54468200, 0.56748200, 0.59087000, 0.61511400,
            0.64056400, 0.66771000, 0.69730300, 0.73062100, 0.77023600, 0.82316600, 1.00000000
        ],
        "ifsc": 1,
        "aces": 1,
        "scalpha": 0.5,
        "scbeta": 1.0,
        "timask1": ":1",
        "timask2": ":2",
        "scmask1": ":1@O2,H12",
        "scmask2": ":2@F1",
        "crgmask": ""
    },

    "aces_setting": {
        "scalpha": 0.5,
        "scbeta": 1.0,
        "gti_cut": 1,
        "gti_output": 0,
        "gti_add_sc": 5,
        "gti_scale_beta": 1,
        "gti_cut_sc_on": 8,
        "gti_cut_sc_off": 10,
        "gti_lam_sch": 1,
        "gti_ele_sc": 1,
        "gti_vdw_sc": 1,
        "gti_cut_sc": 2,
        "gti_ele_exp": 2,
        "gti_vdw_exp": 2,
        "gti_syn_mass": 0
    },
    "slurm_env": [
        "source /etc/profile",
        "module load cuda/11.2",
        "module load mpi/openmpi-4.1.3 ",
        "source $HOME/env/amber22.env"
    ]
}