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 [email protected]: > 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: [email protected] [mailto:[email protected]] >> Im Auftrag von [email protected] >> Gesendet: Donnerstag, 18. Oktober 2012 10:56 >> An: [email protected] >> 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 [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * 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 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
