- ; RUN CONTROL PARAMETERS =
- integrator = md
- ; start time and timestep in ps =
- tinit = 0
- dt = 0.002
- nsteps = 500000
- ; number of steps for center of mass motion removal =
- nstcomm = 1
- comm-grps =
-
- ; LANGEVIN DYNAMICS OPTIONS =
- ; Temperature, friction coefficient (amu/ps) and random seed =
- bd-temp = 300
- bd-fric = 0
- ld-seed = 1993
-
- ; ENERGY MINIMIZATION OPTIONS =
- ; Force tolerance and initial step-size =
- emtol = 100
- emstep = 0.01
- ; Max number of iterations in relax-shells =
- niter = 20
- ; Frequency of steepest descents steps when doing CG =
- nstcgsteep = 1000
-
- ; OUTPUT CONTROL OPTIONS =
- ; Output frequency for coords (x), velocities (v) and forces (f) =
- nstxout = 5000
- nstvout = 5000
- nstfout = 0
- ; Output frequency for energies to log file and energy file =
- nstlog = 5000
- nstenergy = 250
- ; Output frequency and precision for xtc file =
- nstxout-compressed = 250
- compressed-x-precision = 1000
- ; This selects the subset of atoms for the xtc file. You can =
- ; select multiple groups. By default all atoms will be written. =
- compressed-x-grps = Protein
- ; Selection of energy groups =
- energygrps = Protein SOL
-
- ; NEIGHBORSEARCHING PARAMETERS =
- ; nblist update frequency =
- nstlist = 10
- ; ns algorithm (simple or grid) =
- ns-type = grid
- ; Periodic boundary conditions: xyz or none =
- pbc = xyz
- ; nblist cut-off =
- rlist = 0.8
-
- ; OPTIONS FOR ELECTROSTATICS AND VDW =
- ; Method for doing electrostatics =
- coulombtype = cut-off
- rcoulomb-switch = 0
- rcoulomb = 1.4
- ; Dielectric constant (DC) for cut-off or DC of reaction field =
- epsilon-r = 1
- ; Method for doing Van der Waals =
- vdw-type = Cut-off
- ; cut-off lengths =
- rvdw-switch = 0
- rvdw = 0.8
- ; Apply long range dispersion corrections for Energy and Pressure =
- DispCorr = No
- ; Spacing for the PME/PPPM FFT grid =
- fourierspacing = 0.12
- ; FFT grid size, when a value is 0 fourierspacing will be used =
- fourier-nx = 0
- fourier-ny = 0
- fourier-nz = 0
- ; EWALD/PME/PPPM parameters =
- pme-order = 4
- ewald-rtol = 1e-05
- epsilon-surface = 0
-
- ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
- ; Temperature coupling =
- tcoupl = Berendsen
- ; Groups to couple separately =
- tc-grps = Protein SOL
- ; Time constant (ps) and reference temperature (K) =
- tau-t = 0.1 0.1
- ref-t = 300 300
- ; Pressure coupling =
- Pcoupl = Berendsen
- Pcoupltype = Isotropic
- ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
- tau-p = 1.0