[gmx-users] BONDS BREAK DURING MINIMIZATION

[Vidya R]

Hi gromacs users,

The bonds of my organic molecule, break while computing rdf.

The following sentences appear while first minimization

Step 11, time 0.011 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000079 (between atoms 20 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     31     13   37.2    0.1080   0.1080      0.1080
     32     14   32.3    0.1080   0.1080      0.1080

Step 12, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000196 (between atoms 21 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     31     13   45.5    0.1080   0.1080      0.1080
     32     14   38.3    0.1080   0.1080      0.1080

Step 15, time 0.015 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000005, max 0.000318 (between atoms 21 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     31     13   30.7    0.1080   0.1080      0.1080

Step 16, time 0.016 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000043 (between atoms 20 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     31     13   38.4    0.1080   0.1080      0.1080
     32     14   37.0    0.1080   0.1080      0.1080

Step 20, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000143 (between atoms 21 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     31     13   32.5    0.1080   0.1080      0.1080


HOw to fix it?

Thanks,
Vidya.R