[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
Gaurav Chopra
gauravchopra at gmail.com
Mon Apr 17 09:07:29 CEST 2006
Hi
I am getting the following error with mdrun. I have done a few things but
the system complains of 1-4 interactions and gives LINCS warning if the
constraints are not turned off in the mdp file. I also changed the fudgeQQ =
1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4
interaction table size error and then LINCS warning. The output of mdrun for
one of these peptides is as follows. I am working on normal mode decoys of
each peptide and many of the decoys have no problems with mdrun but some
gives this error and Segmentation Fault.
Please advice.
Gaurav
OUTPUT OF MDRUN
Reading file md_1dsl.cl_nH_tir_00710.H_bf.tpr, VERSION 3.3 (single
precision)
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.096062 (between atoms 879 and 882) rms 0.005336
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
starting mdrun 'Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in
water'
100000 steps, 200.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.048269 (between atoms 879 and 882) rms 0.002486
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
895 896 33.7 0.1090 0.1092 0.1090
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001279 (between atoms 882 and 883) rms 0.000069
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
882 883 32.9 0.1011 0.1011 0.1010
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001462 (between atoms 882 and 883) rms 0.000068
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
882 883 34.0 0.1011 0.1011 0.1010
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001105 (between atoms 888 and 890) rms 0.000070
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
882 883 31.8 0.1011 0.1010 0.1010
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001912 (between atoms 888 and 890) rms 0.000096
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
882 883 31.2 0.1010 0.1008 0.1010
Step 20, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.700586 (between atoms 873 and 875) rms 0.023589
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
873 875 90.0 0.1091 0.1854 0.1090
876 878 90.0 0.1090 0.1724 0.1090
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 29473624.000000 (between atoms 873 and 875) rms 776989.562500
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
835 837 34.7 0.1335 0.1732 0.1335
837 838 37.4 0.1010 0.1346 0.1010
837 839 109.7 0.1449 692.1205 0.1449
839 840 111.1 0.1090 692.1713 0.1090
839 841 100.5 0.1529 692.0815 0.1529
839 846 106.7 0.1522 1817.9144 0.1522
841 842 41.8 0.1090 0.1504 0.1090
841 843 41.9 0.1090 0.1508 0.1090
841 844 37.8 0.1410 0.1823 0.1410
846 847 104.8 0.1229 1896.3798 0.1229
846 848 104.1 0.1335 13946.6553 0.1335
848 849 102.0 0.1010 12523.5713 0.1010
848 850 93.4 0.1449 32162.5566 0.1449
850 851 92.5 0.1090 31577.1289 0.1090
850 852 95.3 0.1529 35935.5234 0.1529
850 867 95.0 0.1523 138461.0938 0.1522
852 853 99.7 0.1090 6120.9419 0.1090
852 854 96.8 0.1090 6488.6191 0.1090
852 855 104.6 0.1510 6414.0713 0.1510
855 856 113.0 0.1400 1370.1686 0.1400
855 858 112.2 0.1400 1379.8882 0.1400
856 857 122.2 0.1080 281.0437 0.1080
856 860 121.8 0.1400 280.9830 0.1400
858 859 117.1 0.1080 268.9571 0.1080
858 862 121.6 0.1400 268.9104 0.1400
860 861 31.6 0.1080 0.1373 0.1080
862 863 35.4 0.1080 0.1427 0.1080
867 868 90.7 0.1229 144391.0938 0.1229
867 869 90.2 0.1335 291070.9688 0.1335
869 870 90.3 0.1010 301462.5000 0.1010
869 871 90.5 0.1450 352037.4375 0.1449
871 872 91.2 0.1092 39090.6250 0.1090
871 873 80.9 0.1534 224179.3750 0.1529
871 891 105.9 0.1523 63050.6406 0.1522
873 874 83.6 0.1106 194899.4531 0.1090
873 875 89.0 0.1854 3212625.0000 0.1090
873 876 110.5 0.1526 154736.1719 0.1529
876 877 83.1 0.1104 96243.8906 0.1090
876 878 62.5 0.1724 90734.6406 0.1090
876 879 80.3 0.1534 125826.9609 0.1529
879 880 103.7 0.1100 48631.2148 0.1090
879 881 103.6 0.1093 48326.8906 0.1090
879 882 87.6 0.1467 53880.1172 0.1463
882 883 117.6 0.1009 388.4776 0.1010
882 884 160.2 0.1339 765.5904 0.1340
884 885 67.9 0.1340 475.1604 0.1340
884 888 70.4 0.1339 475.1462 0.1340
885 886 41.1 0.1010 0.1340 0.1010
885 887 40.5 0.1010 0.1327 0.1010
888 889 36.7 0.1011 0.1255 0.1010
891 892 86.4 0.1230 26705.6504 0.1229
891 893 70.7 0.1337 25659.6777 0.1335
893 894 81.4 0.1010 5832.3770 0.1010
893 895 101.2 0.1449 6486.8506 0.1449
895 896 78.8 0.1090 3401.6624 0.1090
895 897 70.5 0.1091 3321.8872 0.1090
895 898 67.6 0.1523 3357.9832 0.1522
898 899 53.8 0.1229 268.3385 0.1229
898 900 63.5 0.1335 268.3486 0.1335
900 901 38.8 0.1010 0.1384 0.1010
900 902 38.0 0.1449 0.1905 0.1449
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