[gmx-users] LINCS WARNING again...

[Luciane Vieira de Mello Rigden]

Dear all,


I'm doing a new simulation and everything was going fine, till
I start the relax_md.

Got the following message:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 625001536.000000 (between atoms 5416 and 5418) rms 10529560.000000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     62     64   42.8    0.1470   0.2101      0.1470
     64     65   40.6    0.1530   0.2100      0.1530
     64     73  113.9    0.1530  12.4138      0.1530
     73     74  124.7    0.1230  12.4545      0.1230
...
   8176   8177   90.0    0.1530   0.6303      0.1530
   8177   8178   90.0    0.1530   0.6087      0.1530
   8177   8179   90.0    0.1530   0.5895      0.1530
Wrote pdb files with previous and current coordinates
step 0Segmentation fault


I have checked the two pdb structure generated:
-rw-r--r--    1 root     root      4534590 Jan 29 13:23 step-1.pdb
-rw-r--r--    1 root     root      4534865 Jan 29 13:23 step0.pdb


The two atoms in the complain message: 5416 and 5418 are part of the
main chain of the protein.
ATOM   5413  CD2 LEU B 565      34.190  60.270  34.320  1.00  0.00
ATOM   5414  C   LEU B 565      30.493  61.182  36.571  1.00  0.00
ATOM   5415  O   LEU B 565      29.665  61.021  35.675  1.00  0.00
ATOM   5416  N   ALA B 566      30.146  61.418  37.833  1.00  0.00
ATOM   5417  H   ALA B 566      30.837  61.460  38.556  1.00  0.00
ATOM   5418  CA  ALA B 566      28.755  61.458  38.309  1.00  0.00
ATOM   5419  CB  ALA B 566      28.885  61.406  39.834  1.00  0.00
ATOM   5420  C   ALA B 566      28.033  62.472  37.418  1.00  0.00
ATOM   5421  O   ALA B 566      26.806  62.423  37.330  1.00  0.00
ATOM   5422  N   SER B 567      28.562  63.694  37.395  1.00  0.00
ATOM   5423  H   SER B 567      29.480  63.874  37.751  1.00  0.00

and I cannot see a  problem with the starting structure.


The gromacs version I am using is 3.1.4.
I've tried to run pr_md and also md, and I got the same message.

Can someone help me?

Thanks in advance.

Luciane