Hi, my problem is, that during the md run the atoms are not frozen somehow. During the minimization run everything worked out fine. But when I did a md run the hydrogen atoms and the other atoms seems to be changes somehow. I calculated the RMSD value and this is why I know that they change. After the minimization the RMSD value between the structure before and after the minimization was about 9.9515e-08 but after the md run the RMSD value was 0.000539742 nm which definitely shows that something was changed. And I want to now why that happened. Because I thought that with the freeze option the atoms which are frozen are not changed.
Thank you >> >> 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 > -- 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
