; ; MD-simulation of 2:1:1 DSPC: SM: CHOL system 256 Lipids ; with Berensen ; 9.5.2007 Samuli Ollila ; Input file ; title = SDPC:SM:CHOL raft cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 30000000 ;total 8 ns. nstcomm = 1 nstxout = 5000 ;10 ps nstvout = 5000 ;10 ps nstfout = 5000 nstlog = 250 ;0.5ps nstenergy = 250 ;0.5ps nstlist = 10 ns_type = grid coulombtype = PME rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 optimize_fft = yes ; nose-hoover temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = PLA SOL CHOL tau_t = 0.1 0.1 0.1 ref_t = 298 298 298 ; Energy monitoring energygrps = PLA SOL CHOL ; Parinello-Rahman pressure coupling is on in two groups Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p = 1.0 1.0 1.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 ref_p = 1.0 1.0 1.0 ; Generate velocites is on at 300 K. gen_vel = no gen_temp = 298.0 gen_seed = 173529