[gmx-users] segmentation fault with lincs warning

ANINDITA GAYEN aninditagayen at yahoo.co.in
Mon Jul 14 07:32:33 CEST 2008

Dear all,

I have an dmpc bilayer equilibrated for 12 ns. I have built a CHAPS molecule in the OPLSAA force field and inserted it in the equilibrated bilayer. There was no problem till the minimisation, but when i started the MD, the job escaped out with a lincs error

Initializing LINear Constraint Solver
  number of constraints is 6572
  average number of constraints coupled to one constraint is 3.3

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.817519   4126   4128   0.017115
        After LINCS         30.145958  17066  17068   1.789056

Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 30.145958 (between atoms 17066 and 17068) rms 1.789056
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4128   4129   31.1    0.1571   0.1600      0.1530
  16859  16858   36.1    0.1529   0.1022      0.1529
  16858  16859   36.1    0.1529   0.1022      0.1529
  16897  16858   49.2    0.1523   0.1495      0.1529
[all the atoms and bonds in the error list are for CHAPS]

Do i have the problem in the topology file? I have inserted 4 chaps mole cules without replacing the dmpc molecules, i.e. 4 chaps with 128 dmpc molecules in the bilayer. Is this causing any steric problem?

Please suggest a way to get out of the problem. If you want, i can upload my topology and mdp files in the next mail.

Yours truly,
anindita gayen

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