[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
HiAttached is part of the gro file which gave the LINCS error on atoms. Thisoutput is the gro file for the initial mdrun, after which final grompp andfinal mdrun was done, which gives the error I described in the message below.Gaurav Gaurav Chopra wrote: 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. you need to minimize better, but if your structures are really bad it won't help either (e.g. when you have a sidechain sticking through a ring) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.sespoel at gromacs.orghttp://folding.bmc.uu.se The lincs warnning are on water molecules isn't it ??? XAvier Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water49GLUHB2 797 4.183 3.686 4.460 49GLU CG 798 4.026 3.813 4.538 49GLUHG1 799 4.042 3.915 4.502 49GLUHG2 800 3.919 3.800 4.550 49GLU CD 801 4.094 3.805 4.672 49GLUOE1 802 4.149 3.697 4.707 49GLUOE2 803 4.086 3.910 4.737 49GLU C 804 4.170 3.865 4.250 49GLU O 805 4.144 3.984 4.263 50MET N 806 4.286 3.822 4.199 50MET H 807 4.301 3.722 4.190 50MET CA 808 4.405 3.904 4.182 50MET HA 809 4.377 4.008 4.198 50MET CB 810 4.510 3.865 4.285 50METHB1 811 4.565 3.777 4.252 50METHB2 812 4.587 3.940 4.292 50MET CG 813 4.452 3.835 4.423 50METHG1 814 4.353 3.796 4.425 50METHG2 815 4.514 3.755 4.462 50MET SD 816 4.453 3.976 4.531 50MET CE 817 4.614 3.925 4.588 50METHE1 818 4.659 3.996 4.655 50METHE2 819 4.599 3.831 4.640 50METHE3 820 4.679 3.909 4.502 50MET C 821 4.467 3.887 4.044 50MET O 822 4.445 3.784 3.981 51PRO N 823 4.549 3.984 4.000 51PRO CA 824 4.626 3.972 3.876 51PRO HA 825 4.553 3.969 3.796 51PRO CB 826 4.711 4.099 3.867 51PROHB1 827 4.810 4.080 3.908 51PROHB2 828 4.721 4.135 3.765 51PRO CG 829 4.639 4.199 3.954 51PROHG1 830 4.708 4.273 3.991 51PROHG2 831 4.564 4.251 3.895 51PRO CD 832 4.572 4.115 4.061 51PROHD1 833 4.644 4.098 4.141 51PROHD2 834 4.483 4.163 4.101 51PRO C 835 4.718 3.850 3.874 51PRO O 836 4.762 3.800 3.978 52SER N 837 4.744 3.801 3.753 52SER H 838 4.711 3.859 3.675 52SER CA 839 4.833 3.689 3.720 52SER HA 840 4.822 3.669 3.614 52SER CB 841 4.978 3.722 3.756 52SERHB1 842 4.988 3.744 3.862 52SERHB2 843 5.041 3.636 3.736 52SER OG 844 5.030 3.825 3.676 52SER HG 845 5.110 3.854 3.717 52SER C 846 4.797 3.559 3.791 52SER O 847 4.884 3.479 3.827 53TYR N 848 4.667 3.537 3.811 53TYR H 849 4.602 3.601 3.770 53TYR CA 850 4.613 3.409 3.852 53TYR HA 851 4.505 3.420 3.851 53TYR CB 852 4.645 3.304 3.741 53TYRHB1 853 4.747 3.275 3.756 53TYRHB2 854 4.589 3.212 3.749 53TYR CG 855 4.643 3.353 3.597 53TYRCD1 856 4.529 3.414 3.540 53TYRHD1 857 4.437 3.421 3.595 53TYRCD2 858 4.764 3.349 3.524 53TYRHD2 859 4.854 3.308 3.568 53TYRCE1 860 4.537 3.471 3.411 53TYRHE1 861 4.452 3.523 3.370 53TYRCE2 862 4.770 3.401 3.394 53TYRHE2 863 4.862 3.395 3.338 53TYR CZ 864 4.656 3.460 3.337 53TYR OH 865 4.662 3.504 3.209 53TYR HH 866 4.747 3.489 3.170 53TYR C 867 4.657 3.374 4.000 53TYR O 868 4.670 3.255 4.028 54ARG N 869 4.682 3.473 4.093 54ARG H 870 4.661 3.565 4.055 54ARG CA 871 4.673 3.444 4.245 54ARG HA 872 4.700 3.339 4.251 54ARG CB 873 4.754 3.510 4.374 54ARG
[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
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' 10 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 0.69 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 0.68 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 0.70 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 0.96 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 29473624.00 (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. 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
Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
Gaurav Chopra wrote: 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. you need to minimize better, but if your structures are really bad it won't help either (e.g. when you have a sidechain sticking through a ring) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-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
Re: [gmx-users] LINCS Warning with MDRUN - Segmentation Fault
On Mon, 17 Apr 2006 00:07:29 -0700 Gaurav Chopra [EMAIL PROTECTED] wrote: 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. The lincs warnning are on water molecules isn't it ??? XAvier ___ gmx-users mailing listgmx-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
