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
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