title = CD3z embbeded in DMPC bi-layer solvated in water. cpp = /usr/bin/cpp integrator = md dt = 0.002 ; ps ! nsteps = 5000000 ; total 10ns. ; Constrain control constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 50000 nstvout = 50000 nstfout = 50000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; nblist update frequency nstlist = 10 ; ns algorithm ns_type = grid rlist = 1 ; Method for doing VdW vdw-type = Cut-off rvdw = 1 ; Method for doing electrostatics coulombtype = PME rcoulomb = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on in three groups Tcoupl = nose-hoover tau_t = 0.3 0.3 0.3 tc-grps = Protein Solvent DMPC ref_t = 310 310 310 ; Pressure coupling is on in two groups Pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p = 3 3 3 3 3 3 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 ; Generate velocites is on at 310 K - do not get velocity from gro file. gen_vel = yes gen_temp = 310 ; Electric field - used ; 100mV/3nm*10E-3v/mV = 0.033 ; E_z = 1 0.033 0.0 ; Energy monitoring energygrps = Protein SOL DMPC ; Center of mass control nstcomm = 1 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = Protein Solvent DMPC