desmond/maestro による MD 計算準備の自動化

ln -s PDBID_addH_delHET_E66K_opt.mae desmond_setup_1.mae

ask {
  task = "desmond:auto"
}

build_geometry {
  add_counterion = {
     ion = Cl
     number = neutralize_system
  }
  add_counterion = {
     ion = Na
     number = neutralize_system
  }
  box = {
     shape = orthorhombic
     size = [10.0 10.0 10.0 ]
     size_type = buffer
  }
  minimize_volume = true   # 手動で追加
  rezero_system = false
  salt = {
     concentration = 0.15
     negative_ion = Cl
     positive_ion = Na
  }
  solvent = SPC
}

assign_forcefield {
}

${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_setup_1 -m desmond_setup_1.msj \
   desmond_setup_1.mae -o desmond_setup_1-out.cms -HOST localhost -TMPLAUNCHDIR -ATTACHED

annealing = false
backend = {
}
bigger_rclone = false
checkpt = {
   first = 0.0
   interval = 240.06
   name = "$JOBNAME.cpt"
   write_last_step = true
}
cpu = 1
cutoff_radius = 9.0
elapsed_time = 0.0
energy_group = false
eneseq = {
   first = 0.0
   interval = 1.2
   name = "$JOBNAME$[_replica$REPLICA$].ene"
}
ensemble = {
   barostat = {
      tau = 2.0
   }
   class = NPT
   method = MTK
   thermostat = {
      tau = 1.0
   }
}
glue = solute
maeff_output = {
   first = 0.0
   interval = 120.0
   name = "$JOBNAME$[_replica$REPLICA$]-out.cms"
   periodicfix = true
   trjdir = "$JOBNAME$[_replica$REPLICA$]_trj"
}
meta = false
meta_file = ?
pressure = [1.01325 isotropic ]
randomize_velocity = {
   first = 0.0
   interval = inf
   seed = 2007
   temperature = "@*.temperature"
}
restrain = none
simbox = {
   first = 0.0
   interval = 1.2
   name = "$JOBNAME$[_replica$REPLICA$]_simbox.dat"
}
surface_tension = 0.0
taper = false
temperature = [
   [300.0 0 ]
]
time = 100000.0
timestep = [0.002 0.002 0.006 ]
trajectory = {
   center = []
   first = 0.0
   format = dtr
   frames_per_file = 250
   interval = 10.0
   name = "$JOBNAME$[_replica$REPLICA$]_trj"
   periodicfix = true
   write_velocity = false
}

# Desmond standard NPT relaxation protocol
# All times are in the unit of ps.
# Energy is in the unit of kcal/mol.
task {
   task = "desmond:auto"
   set_family = {
      desmond = {
         checkpt.write_last_step = no
      }
   }
}

simulate {
   title       = "Brownian Dynamics NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 100ps"
   annealing   = off
   time        = 100
   timestep    = [0.001 0.001 0.003 ]
   temperature = 10.0
   ensemble = {
      class = "NVT"
      method = "Brownie"
      brownie = {
         delta_max = 0.1
      }
   }
   restrain = {
      atom = "solute_heavy_atom"
      force_constant = 50.0
   }
}

simulate {
   effect_if   = [["==" "-gpu" "@*.*.jlaunch_opt[-1]"] 'ensemble.method = Langevin']
   title       = "NVT, T = 10 K, small timesteps, and restraints on solute heavy atoms, 12ps"
   annealing   = off
   time        = 12
   timestep    = [0.001 0.001 0.003]
   temperature = 10.0
   restrain    = { atom = solute_heavy_atom force_constant = 50.0 }
   ensemble    = {
      class  = NVT
      method = Berendsen
      thermostat.tau = 0.1
   }

   randomize_velocity.interval = 1.0
   eneseq.interval             = 0.3
   trajectory.center           = []
}

simulate {
   title       = "NPT, T = 10 K, and restraints on solute heavy atoms, 12ps"
   effect_if   = [["==" "-gpu" "@*.*.jlaunch_opt[-1]"] 'ensemble.method = Langevin']
   annealing   = off
   time        = 12
   temperature = 10.0
   restrain    = retain
   ensemble    = {
      class  = NPT
      method = Berendsen
      thermostat.tau = 0.1
      barostat  .tau = 50.0
   }

   randomize_velocity.interval = 1.0
   eneseq.interval             = 0.3
   trajectory.center           = []
}

solvate_pocket {
   should_skip = true
   ligand_file = ?
}

simulate {
   title       = "NPT and restraints on solute heavy atoms, 12ps"
   effect_if   = [["@*.*.annealing"] 'annealing = off temperature = "@*.*.temperature[0][0]"'
                  ["==" "-gpu" "@*.*.jlaunch_opt[-1]"] 'ensemble.method = Langevin']
   time        = 12
   restrain    = retain
   ensemble    = {
      class  = NPT
      method = Berendsen
      thermostat.tau = 0.1
      barostat  .tau = 50.0
   }

   randomize_velocity.interval = 1.0
   eneseq.interval             = 0.3
   trajectory.center           = []
}

simulate {
   title       = "NPT and no restraints, 24ps"
   effect_if   = [["@*.*.annealing"] 'annealing = off temperature = "@*.*.temperature[0][0]"'
                  ["==" "-gpu" "@*.*.jlaunch_opt[-1]"] 'ensemble.method = Langevin']
   time        = 24
   ensemble    = {
      class  = NPT
      method = Berendsen
      thermostat.tau = 0.1
      barostat  .tau = 2.0
   }

   eneseq.interval   = 0.3
   trajectory.center = solute
}

simulate {
   cfg_file = "desmond_md_job_1.cfg"
   jobname  = "$MASTERJOBNAME"
   dir      = "."
   compress = ""
}

# Job launching command:
# $SCHRODINGER/utilities/multisim -VIEWNAME desmond_molecular_dynamics_gui.MDApp -JOBNAME desmond_md_job_1
# -HOST localhost -maxjob 1 -cpu 1 -m desmond_md_job_1.msj -c desmond_md_job_1.cfg -description 'Molecular Dynamics'
# desmond_md_job_1.cms -mode umbrella -PROJ /home/vagrant/.schrodinger/tmp/tproj36567a6821
# -DISP append -o desmond_md_job_1-out.cms -ATTACHED

"${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_1 -HOST localhost -maxjob 1 -cpu 1 -m desmond_md_job_1.msj
     -c desmond_md_job_1.cfg -description "Molecular Dynamics"
           desmond_md_job_1.cms -mode umbrella
               -o desmond_md_job_1-out.cms -ATTACHED

"${SCHRODINGER}/utilities/multisim" -JOBNAME desmond_md_job_1 -HOST localhost -maxjob 1 -cpu 1 -m desmond_md_job_1.msj
      -c desmond_md_job_1.cfg -description "Molecular Dynamics"
            desmond_md_job_1.cms -mode umbrella  -set 'stage[1].set_family.md.jlaunch_opt=["-gpu"]'
                -o desmond_md_job_1-out.cms -ATTACHED