Hi Tsjerk, Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here.
cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500000 ; total 1000 ps. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 ;fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 pme_order = 4 ;ewald_rtol = 1e-5 ;optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = V-rescale tau_t = 0.1 0.1 tc_grps = Protein SOL ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529
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