Hi Felix, thank you for your answer. So you think that a force of 3.2341940e+02 is okey? To work on?
I also tried to work on with a NVT run but then I got many many LINCS warnings: Step 1114, time 2.228 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000169, max 0.001796 (between atoms 3480 and 3482) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3480 3482 30.3 0.1090 0.1092 0.1090 Step 1121, time 2.242 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000108, max 0.000561 (between atoms 2000 and 2001) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2002 2005 30.4 0.1090 0.1090 0.1090 And in the end there is the error: Fatal error: 11 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposit ion cell of their charge group in dimension x. I looked it up on the GROMACS site and it was written there that such a error is caused by a not well equilibrated system. So I thought that the high force might be the reason. What do you think? Thanks again!! > 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 > -- 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
