Sorry, I forgot to enclose the .mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = PEP MD cpp = /lib/cpp constraints = none integrator = md tinit = 0 dt = 0.002 ; ps ! nsteps = 500000; total 1ns. ;mode for centre of mass motio removal ;comm-mode = linear ;number of steps for centre of mass motion removal nstcomm = 1 nstxout = 5000;output coordinates every 0.5 ps nstvout = 5000Íž output velocities every 0,5ps nstlog = 5000 nstenergy = 250 nstxtcout = 250 xtc-precision = 1000 ;Selection of energy groups
;NEIGHBORSEARCHING PARAMETERES ;nblist update frequency nstlist = 10 ;ns algorithm (simple or grid) ns_type = grid ;nblist cut-off rlist = 0.9 ;domain-decomposition= no ;OPTIONS FOR ELECTROSTATICS AND VDW ;method for doing electrostatics coulombtype = PME rcoulomb = 0.9 ;method for doing van der waals rvdw = 0.9 ;spacing for the PME FFT grid fourierspacing = 0.12 ;FFT grid size fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ;Ewald/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes constraint_algorithm = lincs lincs_order = 4 ;OPTIONS FOR WEAK COUPLING ALGORITHMS ; Berendsen temperature coupling is off in two groups ;TEMPERATURE COUPLING Tcoupl = berendsen tc-grps = Protein ISZ SOL NA+ tau_t = 0.1 0.1 0.1 0.1 ref_t = 310 310 310 310 ;table-extension = 1.2 ; Energy monitoring ;energygrps = Protein ISZ ; Isotropic pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp = 310.0 gen_seed = 173529
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