> > 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
Eva - Sorry, I did not get your question. > 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. Your MDP file should freeze all the atoms in the "Protein-H" index group. Are these atoms actually non-frozen during MD but frozen during geometry optimization at zero-T? Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- 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
