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.
