[gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[ZHANG Cheng]

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"<272699575 at qq.com>;
Date:  Tue, Jan 22, 2019 00:12 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at 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