Hi Eva, The change in energy in every step became smaller than the machine precision can represent (as is stated in the output). In other words: your system is minimized to a very high degree. A value of 10 for the Fmax is very low for a system like yours, even with a pure protein in water system you probably wouldn't hit this value. Furthermore, 30.000 steps for a minimization seems pretty high to me.
Cheers, Felix -----Ursprüngliche Nachricht----- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de Gesendet: Donnerstag, 18. Oktober 2012 10:56 An: gmx-users@gromacs.org Betreff: [gmx-users] question about the minimization Hi everybody, I have a question about the minimization of my protein. For this minimization I fixed the backbone and the membrane atoms which around my protein. I minimized it 30000 steps long but after step 20385 it stops with the output: Steepest Descents converged to machine precision in 20385 steps, but did not reach the requested Fmax < 10. Potential Energy = -8.8805600e+05 Maximum force = 3.2341940e+02 on atom 3050 Norm of force = 2.0930219e+00 I do not see why it can not reach a lower force. I already looked at the structure with Pymol and there I saw that the atom 3050 is in a loop and do not interact with any other residue. My .mdp file looks like this: define = -DPOSRES integrator = steep emtol = 10 nsteps = 30000 nstenergy = 1 energygrps = System coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 rlist = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 pbc = xyz Do you see a reason why it can not reach a force lower than 10? Thank you, Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 * 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
