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

[Fotis Baltoumas]

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
Tel.: +30 2107274876
Mob.: +30 6979258570



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