title = Restrained Apo B2ar with internal water ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 300 ns dt = 0.002 ; 2 fs ; Output control nstxout = 2000 ; save coordinates every 2 ps nstvout = 2000 ; save velocities every 2 ps nstxtcout = 2000 ; xtc compressed trajectory output every 2 ps nstenergy = 2000 ; save energies every 2 ps nstlog = 2000 ; update log file every 2 ps ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ;dihedral restraints dihre = yes dihre_fc = 1000 ; or whatever value you desire dihre_tau = 0.0 nstdihreout = 50 ;distance restraints disre = simple disre_fc = 1000 disre_tau = 100 ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in 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 tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_CCl4 SOL_NA_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_CCl4 SOL_NA_CL