[gmx-users] system and box collapsed

[Qiang Zhong]

Dear users:
     I have a protein complex,which is docking result that from cluspr server,The
complex maybe not perfect,So when I simulate it on gromacs ,many linus warning was
reported.
     Could somebody tell me how to handle this problem,how to pre-optimize the
complex,Thank you very much!



Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002631 (between atoms 2524 and 2525) rms 0.000076
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   63.2    0.1090   0.1092      0.1090
   2524   2525   44.4    0.1090   0.1093      0.1090
   3162   3163   76.0    0.1090   0.1092      0.1090
step 0
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003897 (between atoms 1658 and 1659) rms 0.000089
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   52.8    0.1092   0.1086      0.1090
   2524   2525   37.3    0.1093   0.1088      0.1090
   3162   3163   58.6    0.1092   0.1086      0.1090

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003313 (between atoms 1658 and 1659) rms 0.000085
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   41.0    0.1086   0.1086      0.1090
   2524   2525   31.4    0.1089   0.1088      0.1090
   3162   3163   43.9    0.1087   0.1088      0.1090

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.608712 (between atoms 1658 and 1659) rms 0.008897
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   90.0    0.1087   0.1753      0.1090
   3162   3163   35.5    0.1088   0.1092      0.1090

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.007990 (between atoms 1656 and 1658) rms 0.000219
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   82.2    0.1754   0.1099      0.1090
   3162   3163   44.1    0.1092   0.1095      0.1090

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.429637 (between atoms 1658 and 1659) rms 0.006280
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   90.0    0.1099   0.1558      0.1090
   3162   3163   49.4    0.1095   0.1094      0.1090
....................




------------------------------
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education  
College of Animal Sciences and Technology 
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China