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

[Peter Kroon]

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 <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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