[gmx-users] Lincs warning and writing files

[Amadeu Sum]

I have come across a problem with the Lincs warning messages. My
simulation runs for quite some time and at some point I start to get
the following warning messages:

Step 716120, time 1432.24 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.001645 (between atoms 1790 and 1792) rms 0.000042
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1790   1791   30.5    0.1000   0.1001      0.1000

Step 716122, time 1432.24 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000835 (between atoms 1790 and 1792) rms 0.000023
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1790   1791   30.3    0.1000   0.1000      0.1000
Wrote pdb files with previous and current coordinates

These messages continue at every single step for over 100 ps and they
only stopped because the job crashed due to a full-disk. Looking at
the structure for the atoms in questions, it does seems that for some
reason the molecule is breaking apart (it is a water molecule). My
problem is that once I start getting this warning message, gromacs
writes the configuration to PDB files, and because the simulation did
not crash right away, it continued to write PDB files every single
step thereafter until the disk was full (that created thousands of
files!!!). Is there a way to prevent gromacs from writing all those
PDB files?

Thanks in advance for any help and suggestions,

            --Amadeu