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?
Thanks,
Christian
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