title = Simulated Annealing define = -DPOSRES -DPOSRES_LIPID ; restrain protein and lipid P8 ; Run parameters integrator = md ; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 250000 ; 500 ps ; Bond parameters continuation = no ; starting up constraints = all-bonds ; constrain all bond lengths constraint-algorithm = lincs ; holonomic constraints lincs-iter = 1 ; accuracy of LINCS lincs-order = 4 ; also related to accuracy ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstfout = 1000 ; save forces every 2 ps nstenergy = 1000 ; save energies every 2 ps ; Neighborsearching nstlist = 5 ; 10 fs ns_type = grid ; search neighboring grid cells rlist = 1.2 ; short-range neighborlist cutoff (nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (nm) rvdw = 1.2 ; short-range van der Waals cutoff (nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on in three groups Tcoupl = Berendsen ; Weak coupling tc_grps = Protein_DPPC Water_and_ions ; two groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling Pcoupl = Berendsen ; Weak coupling Pcoupltype = semiisotropic ; uniform scaling of x-y vectors, independent z ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Generate velocities is off gen_vel = no ; Velocity generation is off ; Periodic boundary conditions are on in all directions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC Water_and_ions ; Simulated annealing annealing = single single single ; single sequence of points for each T-coupling group annealing_npoints = 2 2 2 ; two points - start and end temperatures annealing_time = 0 500 0 500 0 500 ; time frame of heating - heat over period of 500 ps annealing_temp = 0 323 0 323 0 323 ; start and end temperatures