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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php