[gmx-users] LINCS warnings for bonds that do not exist

Christian Blouin cblouin at cs.dal.ca
Thu Aug 2 15:57:28 CEST 2012

My simulation aborts rather quickly because it accumulates too many
LINCS warning. I checked the various plots and everything seems to be
stable (temperature, pressure, total energy, etc.). The stderr gives
me warnings looking like this:

Step 2304252, time 4608.5 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.043352, max 0.606635 (between atoms 150 and 151)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    150    152   90.0    0.0985   0.1490      0.1000
    150    151   90.0    0.1314   0.1607      0.1000

The problem I see is that atom 150 and 151 do not even have a bond
between them (they are the two hydrogens of one water molecule). I
also get similar warning between 150 and 152, which are not even on
the same water molecule. I have extensively equilibrated the system as
I thought that it was the problem originally.

Anyone here has an intuition as to why this may happen?



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