HI everybody, I want to do a minimization and a md run with my protein. But I only want the hydrogen atoms to be minimized but not the rest of the protein. I use the freezegrps = Protein-H freezedim = Y Y Y
option in my mdp files to make sure that they don't change. During the minimization steps everything works fine and it really does not change. But now I started the md run and here the protein somehow get minimized too. I do not understand why everything works fine during the minimization but not during the md run. My mdp file for the md run looks like this: define = -DPOSRES integrator = md dt = 0.001 nsteps = 5000 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 500 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp = 200.0 gen_seed = 9999 constraints = all-bonds tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no freezegrps = Protein-H freezedim = Y Y Y Are there any problems in this file? I don't see any problems. Thank you, Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
