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

[Peter Kroon]

Hi all,


@Fotis, the softcore potential for minimization sounds interesting, I'll
remember that!

Alternatively, something we also occasionally do in the lab, is replace
all constraints for stiff bonds during minimization and if needed the
first bit of equilibration.


Peter

On 22-01-19 13:24, Fotis Baltoumas wrote:
> Hello all,
>
> I would like to point out step 2 of the original poster's message:
>
>>> /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./
>
> I've found, from personal experience, that this message ("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") means that:
>
> 1. either there is something wrong with the system structure or
> topology (a fact shown at almost the first step of an equilibration
> following the minimization with this message).
>
> 2. or that single precision GROMACS cannot perform minimization
> properly.  The latter often applies to MARTINI systems, especially if
> they are large or have too many protein subunits (I can't say whether
> the application of ELNEDYN plays a part).
>
> If, hopefully, the latter case applies, the solution is to either use
> double precision GROMACS for minimization (gmx_d mdrun) or, since this
> is MARTINI, use "soft" potential modifiers like those they apply in
> the mdp files given by the CHARMM-GUI Martini Maker.  In any case, the
> initial minimization should be followed by a second, "standard" one
> (i.e. standard mdp options and single precision GROMACS).
>
> Hope this helps in some manner,
>
> Fotis Baltoumas
>
>  --
> Fotis A. Baltoumas, Bsc, Msc
> Phd Candidate, Bioinformatics Postgraduate Programme
> Section of Cell Biology and Biophysics
> Department of Biology
> National & Kapodistrian University of Athens
> Panepistimiopolis, Athens 157 01, GREECE
>    --------------------------------------
>
> email : fbaltoumas at biol.uoa.gr
> http://biophysics.biol.uoa.gr
> http://bioinformatics.biol.uoa.gr
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>
>
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