[gmx-users] gmxcheck error!!!

[nanyu101]

Dear gmx_users,
  I have tried to equilibrate lipid bilayer dppc128.pdb.The results listed as follows:

Steepest Descents converged to 250 in 1399 steps
  Potential Energy  = -2.76143e+05
Maximum force:  1.24819e+02

Off course I think I succeeded in minimizing the bilayer.

  But when I tried to run mdrun, the system failed.

Step 6567, time 13.134 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1453810.750000 (between atoms 6065 and 6066) rms 34077.503906
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   6054   6055   35.4    0.1470   0.1831      0.1470
   6055   6056  120.0    0.1530  52.4671      0.1530
   6056   6057   92.4    0.1430 264.8736      0.1430
   6057   6058  102.1    0.1612 1650.0942      0.1610
   6058   6059   92.7    0.1481 1678.7709      0.1480
   6058   6060  108.9    0.1482 1515.9398      0.1480
¡­¡­¡­¡­¡­¡­¡­¡­¡­¡­¡­¡­¡­¡­..

6087   6088  115.6    0.1530  22.8513      0.1530
   6088   6089   36.2    0.1530   0.1926      0.1530
./f: line 4: 32197 Segmentation fault      mdrun -v -deffnm test


And then I tried to use gmxcheck -c dppc_em.pdb to check the structure, the system told as follows:
Atoms outside box ( 6.4184 6.4435 6.5965 ):
(These may occur often and are normally not a problem)
atom# name  residue r_vdw  coordinate
  879  C30  DPP  17 0.15    2.11   6.51   3.31
  880  C31  DPP  17 0.15    2.09   6.54   3.46
  909  O10  DPP  18 0.105   1.88 -0.007   1.45
  931  C32  DPP  18 0.15    2.08 -0.072   1.92
  932  O33  DPP  18 0.105   1.97 -0.127      2
  933  C34  DPP  18 0.15    1.87 -0.187   1.94
  934  O35  DPP  18 0.105   1.85 -0.203   1.82
  935  C36  DPP  18 0.15    1.77 -0.227   2.05
  936  C37  DPP  18 0.15    1.62 -0.211      2
  937  C38  DPP  18 0.15    1.53 -0.244   2.12
(maybe more)


I don't know what had happen.
Any comments are appreciated!!!

Best wishes,
Xianhui Wu

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