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
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