[gmx-users] (no subject)

[黄永棋]

Hi 

  I was trying to do a protein simulation with the protein embedded in a dopc bilayer , but the mdrun killed with a message like this:

"  Step 124772, time 249.544 (ps)  LINCS WARNING
   relative constraint deviation after LINCS:
   max 78.497551 (between atoms 28341 and 28343) rms 0.598885
   bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
   28332  28333  170.9    0.1000   0.9127      0.1000
   28335  28336   30.4    0.1000   0.7634      0.1000
   28335  28337  179.8    0.1000   6.4688      0.1000
   28341  28342  140.6    0.1000   0.7312      0.1000
   28341  28343  179.7    0.1000   7.9498      0.1000
   Constraint error in algorithm Lincs at step 124772 
   Wrote pdb files with previous and current coordinates

   Segmentation fault  "


I checked the gro. file and found these are water molucules . Can anybody tell me why this  happened and what  shall I do to aviod this ?

Thanks  in advance.


Yongqi Huang




黄永棋
2007-04-09
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070409/662dee7e/attachment.html>