Hi,
You can reduce the timestep during equilibrations to e.g. 10 fs, or 5 when you have a really bad starting configuration. Bring it back up to 20 (in steps if needed) before starting your actual equilibration/production though. In addition, you can raise the lincs_order to 8. And yes, the cgmartini.nl forum is currently unavailable due to technical issues. We're working on it. Peter On 22-01-19 10:07, Mark Abraham wrote: > Hi, > > I don't have any experience of coarse-grained systems, but everything looks > OK from this level. It is normal to troubleshoot by visualizing your input > and progress result. Minimizers are local, so if you start from something > that has a frustration that can't be resolved, you are stuck. Generally > this can be seen. > > Mark > > On Mon, 21 Jan 2019 at 22:59 ZHANG Cheng <272699...@qq.com> wrote: > >> I also tried to reduce the "emtol" gradually in the mdp file, i.e. from >> 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at >> "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS >> warnings". >> >> >> Then I looked at the edr files. >> The potential in "emtol = 1000" and "emtol = 100" runs were actually >> converging >> >> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png >> >> >> My understanding for the "LINCS warnings" is, the system is not stable. >> But why the potential is still converging? >> >> >> Do I need to adjust the "lincs warning threshold", or "set the environment >> variable GMX_MAXCONSTRWARN to -1"? How to do that? >> >> >> Is there a "standard" mdp file for minimization for a coarse-grained >> system with 10 proteins in water? >> I am using this, but I do not know how to modify it. >> >> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp >> >> >> >> >> ------------------ Original ------------------ >> From: "ZHANG Cheng"<272699...@qq.com>; >> Date: Tue, Jan 22, 2019 00:12 AM >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; >> >> Subject: "Too many LINCS warnings" in a minimization after solvation with >> coarse-grained waters >> >> >> >> I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was >> told "Too many LINCS warnings" in the minimization after solvation with >> coarse-grained waters. >> >> >> I try to diagnose the problems based on >> >> http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up >> >> >> My procedure is >> >> >> 1) A single CG-protein was firstly minimized in vacuum, no problem >> >> >> 2) Then 10 of this protein were inserted to a box, followed by a >> minimization. It "stopped because the algorithm tried to make a new step >> whose size was too small, or there was no change in the energy since last >> step." So I think this minimization is also successful. >> >> >> 3) The system was then solvated by >> $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro >> -radius 0.21 -o system-solvated.gro -p system.top >> >> >> 4) Then the solvated system is minimized by >> $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p >> system.top -o system-min-solvent.tpr >> $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro >> >> PDB structures were outputted from step 327 to step 710, and it stopped >> due to the "LINCS warnings". >> >> >> The "minimization_solvate.mdp" is here >> >> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp >> >> >> The "system-min-solvent.log" is here >> >> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log >> >> >> So I think the system with 10 proteins in vacuum is okay (right?). But >> when CG-water is added, it got problem? How to modify my system? Let me >> know if you need other information. Thank you. >> >> >> Cheng >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.