Dear all,

One of my GROMACS MD simulations crashed after running stably for almost 4ns (=several
weeks on our system). The error message I get is this:

"...
LINCS WARNING
relative constraint deviation after LINCS:
max 0.000987 (between atoms 3286 and 3289) rms 0.000026
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
..."

I got almost 100 of these LINCS WARNINGs before the system eventually crashed.
The atoms involved (3286 and 3289) belong to a protonated lysine residue, the topology
of which was generated in the standard (pdb2gmx) way.
Does anybody have suggestions as to what I could do to get round this problem ?
Do you think there is anything wrong with the lysine residue or anything else ?


I would be grateful for any advice you could give me. Thanks very much !

Best wishes,
Chris


Christoph Meier

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Christoph Meier
Membrane Protein Simulation Group
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3BW
U.K.
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