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

[Mark Abraham]

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 <272699575 at 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"<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
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