Hi there,
I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form and it didn't unfold. I know it may need longer time, but it doesn't show any sign of even starting to unfold. I think I am restraining the protein in some way. Please see below the content of ~.mdp file that I use. Would you please let me know how I could unfold a protein using an MD simulation? Do you think unfolding a water soluble protein in vacuum would be faster? Cheers, Siavoush cpp = /lib/cpp include = -I../top integrator = md dt = 0.002 nsteps = 500000 nstxout = 1000 nstvout = 1000 nstlog = 100 nstenergy = 100 nstxtcout = 100 xtc_grps = protein sol energygrps = protein sol nstlist = 10 ns_type = grid rlist = 0.8 coulombtype = cut-off rcoulomb = 1.4 rvdw = 1.4 pbc = xyz tcoupl = berendsen tc-grps = protein sol tau_t = 0.1 0.1 ref_t = 400 400 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 400 gen_seed = 173529 constraints = all-bonds _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
