I think your RMSD of 0.000539742 is quite a small value, which can be, at least theoretically, caused by the accumulation of errors. Can you simulate your protein for a longer time to show that RMSD is indeed significant?
On Sat, Jul 28, 2012 at 1:01 AM, <reising...@rostlab.informatik.tu-muenchen.de> wrote: > 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 >> > > -- 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
