Hi Berk, thank you for the reply here is my mdp file:
; ; User aneamtu ; Joi, 7 mai - 2009 ; Input file ; title = Production_runs ;define = -DPOSRES -DPOSRES_CA2+_IONS ;constraints = all-bonds integrator = md dt = 0.001 nsteps = 50000 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 500 nstxtcout = 50 xtc_grps = Protein_ions nstenergy = 100 nstlist = 10 ns_type = grid coulombtype = PME rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 optimize_fft = yes Tcoupl = v-rescale tc-grps = Protein SOL ions tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 energygrps = Protein SOL CA2+ NA+ CL- Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no gen_temp = 310.0 gen_seed = 173529 pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 2 pull_group0 = Protein pull_group1 = CA2+1 pull_rate1 = 0.3 pull_group2 = CA2+2 pull_rate2 = 0.3 I do not understand what I do wrong.. Should I use a -pi pull.ppa file like in gromacs 3.x ? Andrei _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php