[gmx-users] Error: relative constraint deviation after LINCS

[raja]

Dear GMXIONS, 
    For the simulation of ligand-enzyme complex. At the position
    restraints step , I got these following error. More I had already
    simulated the same protein for 2ns without the bound ligand. But I
    suspect these error are due to addition of ligand or for some other
    reason, 

The same error are discussed elsewhere in discussion forum but I could
not get conclution for my problem. So please
help me.

The Error part 
##########################################################################################################
step 0
Step 10, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002406 (between atoms 2664 and 2666) rms 0.000090
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2664   2665   31.5    0.1090   0.1091      0.1090
step 30, will finish at Tue Mar 28 14:14:30 2006
Step 38, time 0.076 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.296349 (between atoms 2576 and 2577) rms 0.004434
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2576   2577   90.0    0.1090   0.1413      0.1090
   2578   2579   90.0    0.1090   0.1180      0.1090

Step 39, time 0.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 4821.659668 (between atoms 2584 and 2585) rms 70.115692
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2557   2559  104.4    0.1450   0.5221      0.1449
   2559   2560   87.2    0.1090   0.5446      0.1090
   2559   2561  118.5    0.1530   0.5012      0.1529
   2559   2572   99.8    0.1523   1.4141      0.1522
   2561   2562   82.9    0.1090   0.0423      0.1090
   2561   2563   69.9    0.1091   0.0341      0.1090
   2561   2564   34.2    0.1529   0.0840      0.1529
   2572   2573   88.1    0.1231   1.5691      0.1229
   2572   2574  110.8    0.1335   6.8042      0.1335
   2574   2575  106.0    0.1010   6.5640      0.1010
   2574   2576   81.3    0.1456   8.8651      0.1449
   2576   2577   41.1    0.1413   5.5404      0.1090
   2576   2578  112.6    0.1532  12.6753      0.1529
   2576   2588  100.3    0.1526  10.1017      0.1522
   2578   2579   87.1    0.1180  54.2609      0.1090
   2578   2580   92.4    0.1534  18.2981      0.1529
   2578   2584   88.1    0.1538  35.5616      0.1529
   2580   2581   89.1    0.1092   1.3620      0.1090
   2580   2582   90.1    0.1090   1.4119      0.1090
   2580   2583   88.1    0.1091   1.2295      0.1090
   2584   2585   90.0    0.1090 525.6699      0.1090
   2584   2586   91.5    0.1089  23.0823      0.1090
   2584   2587   92.0    0.1089  22.9080      0.1090
   2588   2589  104.3    0.1229   3.1250      0.1229
   2588   2590  115.1    0.1335   2.8415      0.1335
   2590   2591  109.1    0.1450   0.9337      0.1449
   2590   2599  108.6    0.1450   0.9203      0.1449
   2591   2592  112.4    0.1090   0.3062      0.1090
   2591   2593  108.3    0.1529   0.2859      0.1529
   2591   2602  120.1    0.1522   0.2576      0.1522
   2593   2594   43.8    0.1090   0.1570      0.1090
   2593   2595   45.3    0.1090   0.1562      0.1090
   2596   2597   30.6    0.1090   0.1273      0.1090
   2596   2598   41.2    0.1090   0.1451      0.1090
   2596   2599   96.6    0.1529   0.1996      0.1529
   2599   2600  133.4    0.1090   0.2447      0.1090
   2599   2601  135.4    0.1090   0.2755      0.1090
   2602   2603   32.1    0.1229   0.1593      0.1229
   2602   2604   32.6    0.1335   0.1740      0.1335
Segmentation fault (core dumped)
###############################################################################################

With thanks !
B.Nataraj

 
-- 
  raja
  raja_28 at fastmail.us

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