# example run input file for the the equilibrium simulation
# use with 
#   - mdpow-equilibrium
#   - mdpow-fep
#
# Note: enclose strings (especially names) with quotes.

DEFAULT:
    qscripts: "local.sh"

setup:
    name: "benzene"
         # common, descriptive name, e.g. benzene
    molecule: "BNZ"
         # Gromacs [ molecule ] identifier from the itp file (typically a 3-letter code)
    watermodel: "tip4p"
         # water model available in Gromacs (OPLS-AA):
         # tip4p, tip5p, tip3p, spc, spce     
    itp: "benzene/benzene.itp"
         # Gromacs itp file name 
    structure: "benzene/benzene.pdb"
         # coordinate file name (pdb, gro, ... anything that Gromacs can read)
    distance:  None
         # minimum distance between solute and box face (by default
         # (None) this is set to a 1.0 nm for water and 1.5 nm for
         # other solvents)    
    boxtype: dodecahedron
         # box type understood by Gromacs 'gmx editconf' (cubic,
         # triclinic, octahedron, dodecahedron    
    maxwarn: 0
         # maximum number of warnings tolerated by grompp during setup
    gromacsoutput: True
         # True: print output from Gromacs command to screen (useful for debugging)
         # False: only show the MDPOW messages

# energy minimization

energy_minimize:
    mdp: "em_opls.mdp"
         # run parameter file for Gromacs;
         # (will be searched as (1) absolute path, (2) in current directory (3)
         # in the package templates)


# short simulation with a time step of 0.1 fs to gently relax steric clashes

MD_relaxed:
    qscript: "local.sh"
         # queuing system scripts to produce
    runlocal: True
         # True: launch Gromacs mdrun and wait for it
         # False: produce queuing system scripts and stop
    runtime: 1
         # run time in ps
    mdp: "NPT_opls.mdp"
         #  run parameter file for Gromacs;
         # (will be searched as (1) absolute path, (2) in current directory (3)
         # in the package templates)
         # special index groups  __main__ __environment__ can be used

# equilibrium simulation at constant temperature and pressure with a
# time step of 2 fs.

MD_NPT:
    qscript: "local.sh"
         # queuing system scripts to produce
    runtime: 10
         # simulation run time in ps (for this example, a VERY short
         # run time was used; for real work, this must be many ns)
    runlocal: True
         # True: launch Gromacs mdrun and wait for it
         # False: produce queuing system scripts and stop
    mdp: "NPT_opls.mdp"
         # run parameter file for Gromacs;
         # (will be searched as (1) absolute path, (2) in current directory (3)
         # in the package templates)
         # special index groups  __main__ __environment__ can be used

FEP:
    method: "BAR"
         # BAR or TI
    qscript: "local.sh"
         # queuing system scripts to produce
    runtime: 25
         # run time in ps for each free energy window (the run time
         # for this example is VERY short)
    runlocal: True
         # True: launch Gromacs mdrun and run all windows in a serial fashion
         # False: produce queuing system scripts and stop
    maxwarn: 1
         # maximum number of warnings tolerated by grompp during setting up FEP runs
         # Set to 1 if you want to ignore the warning (in 4.6.x):
         #
         # WARNING 1 [file md.mdp]:
         #  With coulomb soft core, the reciprocal space calculation will not
         #  necessarily cancel.  It may be necessary to decrease the reciprocal space
         #  energy, and increase the cutoff radius to get sufficiently close matches
         #  to energies with free energy turned off.
    mdp: "bar_opls.mdp"
         # run parameter file for Gromacs;
         # (will be searched as (1) absolute path, (2) in current directory (3)
         # in the package templates)
         # special index groups  __main__ __environment__ can be used

FEP_schedule_Coulomb:
    name: "Coulomb"
    description: "dis-charging vdw+q --> vdw"
    label: "Coul"
    couple_lambda0: "vdw-q"
    couple_lambda1: "vdw"
         # soft core alpha: linear scaling for coulomb (sc_alpha = 0)
         # ignore the other sc_*
    sc_alpha: 0
    sc_power: 1
    sc_sigma: 0.3
    lambdas: 0, 0.25, 0.5, 0.75, 1.0

FEP_schedule_VDW:
    name: "vdw"
    description: "decoupling vdw --> none"
    label: "VDW"
    couple_lambda0: "vdw"
    couple_lambda1: "none"
         # recommended values for soft cores (Mobley, Shirts et al)
    sc_alpha: 0.5
    sc_power: 1
    sc_sigma: 0.3
    lambdas: 0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1


# options to control a mdrun process
mdrun:
    stepout: 1000
         # how often to report progress (-stepout)
    verbose: True
         # report progress verbosely (True is -v)
    nice: 19
         # nicel level
    maxthreads: None
         # maximum number of threads (-nt), 0 or None lets mdrun automatically choose
