read
   #mol pqr gly.pqr
   #mol pqr gly2.pqr
    mol pqr gly_cg.pqr
    mol pqr gly_cg2.pqr
end
elec name comp_solv        # Gly
    pbsam-auto

    runtype dynamics        # Can be energyforce, electrostatics etc
    runname dyn_gly         # Output name for files created by program

    units kT
    ## info for molecule
    #mesh skin
    tolsp 2.5

   #imat imat/mol0sph
   #imat imat/mol1sph

   #exp exp/mol0
   #exp exp/mol1

    termcombine or
    term time 560.0
    ntraj 2

    # WARN: diff with a number is not supported in pbsam-auto
    # diff 1 move 0.45 0.001
    diff move 0.45 0.001
    # WARN: diff with a number is not supported in pbsam-auto
    # diff 2 stat
    diff stat

    xyz 1 traj_1_1.xyz
    xyz 1 traj_1_2.xyz

    xyz 2 traj_2_1.xyz
    xyz 2 traj_2_2.xyz

    temp 298.15                                       # System temperature (K)
    pdie 4.0                                          # Solute dielectric                 
    sdie 80.0                                         # Solvent dielectric                
    # WARN: ion is not supported in pbsam-auto
    # ion charge 0.0 conc 0.05 radius 0.0               # Monovalent salt conc in M

end

quit

