Hi Erik, 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 And yes, I use constraints. I have a membrane represented by dummy atoms around my protein. They are fixed and I also fixed the backbone. Or is that a problem. Thank you , Eva > It could be due to your mdp-settings. What's your time step? Do you use > constraints and virtual interaction sites? > > Erik > > 18 okt 2012 kl. 12.04 skrev reising...@rostlab.informatik.tu-muenchen.de: > >> 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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
