title = MD simulation of OR1G1 with full explicit membrane and solvant ; Preprocessing cpp = /lib/cpp define = -DPOSRE ; Run parameters integrator = md dt = 0.002 nsteps = 5000 ; 10 ps for PR2 nstcomm 1 comm_mode = linear ; File outuput nstxout = 500 nstvout = 250 nstlog = 250 nstenergy = 250 nstxtcout = 500 ; Molecule decomposition xtc_grps = Protein 478 SOL CL- energygrps = Protein 478 SOL CL- nstlist = 5 ns_type = grid pbc = xyz rlist = 0.9 ; Electrostatics & VdW coulombtype = PME pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes ; try to get some time left for long simulations rcoulomb = 0.9 rvdw = 1.4 vdwtype = Cut-off ; Temperature tcoupl = berendsen tc-grps = Protein 478 SOL CL- tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 ; Pression Pcoupl = berendsen Pcoupltype = isotropic tau_p = 10 ref_p = 1.0 compressibility = 4.5e-5 ; Velocities while at 300 K gen_vel = no gen_temp = 300 gen_seed = -1 ; Constraints constraints = all-bonds constraint_algorithm = lincs freezegrps = Protein-H freezedim = Y Y Y