[gmx-users] Change only one atom pair VdW interaction
Hello, I wanted to know if one can change the VdW epsilon for just one atom pair. If suppose my system has only carbons, hydrogen and oxygen and if I just want to change the epsilon for C-O interaction for VdW without effecting anything else, i.e. not changing C-C interaction for the oplsaa forcefield, is there a way to do this without modifying the code? As epsilon_H = 0, the only thing which will be effected by changing epsilon_C would be C-O and C-C interaction, but I do not want to change C-C interaction but only C-O interaction. Thanks, Gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: LINCS Warning with MDRUN - Segmentation Fault (Gaurav Chopra)
Hi Attached is part of the gro file which gave the LINCS error on atoms. This output is the gro file for the initial mdrun, after which final grompp and final 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 itwon'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, Swedenphone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://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 water 49GLU HB2 797 4.183 3.686 4.460 49GLU CG 798 4.026 3.813 4.538 49GLU HG1 799 4.042 3.915 4.502 49GLU HG2 800 3.919 3.800 4.550 49GLU CD 801 4.094 3.805 4.672 49GLU OE1 802 4.149 3.697 4.707 49GLU OE2 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 50MET HB1 811 4.565 3.777 4.252 50MET HB2 812 4.587 3.940 4.292 50MET CG 813 4.452 3.835 4.423 50MET HG1 814 4.353 3.796 4.425 50MET HG2 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 50MET HE1 818 4.659 3.996 4.655 50MET HE2 819 4.599 3.831 4.640 50MET HE3 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 51PRO HB1 827 4.810 4.080 3.908 51PRO HB2 828 4.721 4.135 3.765 51PRO CG 829 4.639 4.199 3.954 51PRO HG1 830 4.708 4.273 3.991 51PRO HG2 831 4.564 4.251 3.895 51PRO CD 832 4.572 4.115 4.061 51PRO HD1 833 4.644 4.098 4.141 51PRO HD2 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 52SER HB1 842 4.988 3.744 3.862 52SER HB2 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 53TYR HB1 853 4.747 3.275 3.756 53TYR HB2 854 4.589 3.212 3.749 53TYR CG 855 4.643 3.353 3.597 53TYR CD1 856 4.529 3.414 3.540 53TYR HD1 857 4.437 3.421 3.595 53TYR CD2 858 4.764 3.349 3.524 53TYR HD2 859 4.854 3.308 3.568 53TYR CE1 860 4.537 3.471 3.411 53TYR HE1 861 4.452 3.523 3.370 53TYR CE2 862 4.770 3.401 3.394 53TYR HE2 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 HB1 874 4.855 3.504 4.327 54ARG HB2 875 4.748 3.618 4.351 54ARG CG 876 4.730 3.461 4.557 54ARG HG1 877 4.799 3.379 4.533 54ARG HG2 878 4.812 3.521 4.599 54ARG CD 879 4.604 3.380 4.698 54ARG HD1 880 4.559 3.315 4.625 54ARG HD2 881 4.667 3.298 4.735 54ARG NE 882 4.459 3.405 4.816 54ARG HE 883 4.508 3.338 4.886 54ARG CZ 884 4.385 3.397 4.953 54ARG NH1 885 4.342 3.454 4.851 54ARG HH11 886 4.441 3.411 4.820 54ARG HH12 887 4.246 3.444 4.821 54ARG NH2 888 4.261 3.401 5.023 54ARG HH21 889 4.246 3.370 5.123 54ARG HH22 890 4.176 3.464 5.021 54ARG C 891 4.534 3.490 4.285 54ARG O 892 4.460 3.564 4.222 55GLY N 893 4.517 3.462 4.410 55GLY H 894 4.605 3.428 4.447 55GLY CA 895 4.425 3.510 4.506 55GLY HA1 896 4.471 3.539 4.600 55GLY HA2 897 4.375 3.599 4.478 55GLY C 898 4.336 3.393 4.525 55GLY O 899 4.363 3.279 4.483 56ARG N 900 4.226 3.424 4.591 56ARG H 901 4.219 3.519 4.627 ___ gmx-users mailing listgmx-users
[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
[gmx-users] Range Checking error
Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file: nsgrid.c, line: 226 // // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot // put these on a grid, so this is usually where we detect those errors. // Make sure your system is properly energy-minimized and that the potential // energy seems reasonable before trying again. /Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00 bonds that rotated more than 30 degrees: also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav / // Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] // Please report this to the mailing list (gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users) // --- // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // 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 gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / -- 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.se http://www.gromacs.org/mailman/listinfo/gmx-users spoel at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] LINCS Warning using mdrun
Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ 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
[gmx-users] Range Checking Error
//
// Range checking error:
// Explanation: During neighborsearching, we assign each particle to a grid
// based on its coordinates. If your system contains collisions or parameter
// errors that give particles very high velocities you might end up with some
// coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// put these on a grid, so this is usually where we detect those errors.
// Make sure your system is properly energy-minimized and that the potential
// energy seems reasonable before trying again.
/Please follow the advice in the above two sentences. Check your structure.
I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
bonds that rotated more than 30 degrees:
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy = 250
nstxtcout = 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = TRUE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 20
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed = 815131
rlist = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 51456
ref_t: 300
tau_t: 1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
CPU= 0, lastcg= 8223, targetcg= 4112, myshift= 0
nsb-shift = 1, nsb-bshift= 0
Neighbor Search Blocks
nsb-nodeid: 0
nsb-nnodes: 1
nsb-cgtotal: 8224
nsb-natoms: 24594
nsb-shift: 1
nsb-bshift: 0
Nodeid index homenr cgload workload
0 0 24594 8224 8224
Max number of graph edges per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm
[gmx-users] Range Checking Error
/ //
// // Range checking error:
// // Explanation: During neighborsearching, we assign each particle to a grid
// // based on its coordinates. If your system contains collisions or
parameter
// // errors that give particles very high velocities you might end up with
some
// // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// // put these on a grid, so this is usually where we detect those errors.
// // Make sure your system is properly energy-minimized and that the
potential
// // energy seems reasonable before trying again.
// /Please follow the advice in the above two sentences. Check your structure.
//
// I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
// and steep using -DFLEXIBLE in my mdp file and I was able to compute using
mdrun but I got the following in my log file
//
// Initiating Steepest Descents
// Center of mass motion removal mode is Linear
// We have the following groups for center of mass motion removal:
// 0: rest, initial mass: 24594
// Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
// Removing pbc first time
// Done rmpbc
// Steepest Descents:
//Tolerance (Fmax) = 1.0e+01
//Number of steps=1
// Grid: 10 x 10 x 20 cells
// Configuring nonbonded kernels...
// Testing AMD 3DNow support... not present.
// Testing ia32 SSE support... present.
//
//
// Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
// I get the following
//
// Step 0, time 0 (ps) LINCS WARNING
// relative constraint deviation after LINCS:
// max 1391229833052160.00 (between atoms 655 and 657) rms
40665803128832.00
// bonds that rotated more than 30 degrees:
/
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy= 250
nstxtcout= 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= TRUE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 20
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed= 815131
rlist= 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau= 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 1e-04
lincs_order =
[gmx-users] Re: LINCS Warning using mdrun
/ Hi // // I get the following error when using mdrun for a protein in solution. // I have checked the structure and everything looks fine to me. Could // you suggested anything else I could do. / How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen --- Hi I used the initial minimization run using grompp and mdrun using steepest descent for 400 steps and 0.002 ps as the step size. The constraints are all-atom. The following is the output from the log file that was generated after the md. Any suggestions? Thanks Gaurav --- mdrun log file output -- Initializing LINear Constraint Solver number of constraints is 934 average number of constraints coupled to one constraint is 3.6 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.608377894898 0.031756 After LINCS 0.126305892894 0.007000 Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 Going to use C-settle (6845 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074 rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.115310685686 0.023558 After LINCS 0.115624892894 0.006694 Started mdrun on node 0 Tue Mar 14 04:21:35 2006 Initial temperature: 299.541 K Step Time Lambda 00.00.0 Grid: 12 x 12 x 12 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. There are 21469 atoms in your xtc output selection Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 10.170899898899 0.711794 After LINCS 3.372058894895 0.239340 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 883886 36.70.1540 0.2007 0.1529 886887 36.80.1098 0.1474 0.1090 886888 43.60.1099 0.1575 0.1090 886889 51.70.1526 0.2510 0.1529 889890 60.60.1097 0.1917 0.1090 889891 66.20.1096 0.2043 0.1090 889892 44.60.1561 0.0485 0.1463 892893 55.70.1042 0.1304 0.1010 894895 54.60.1221 0.5859 0.1340 894898 135.90.1495 0.4473 0.1340 895896 77.60.1051 0.0671 0.1010 895897 40.40.1011 0.1018 0.1010 898899 40.00.0997 0.3249 0.1010 903905 40.20.1453 0.1959 0.1449 905906 45.20.1093 0.1556 0.1090 905907 65.60.1542 0.3041 0.1529 905921 35.00.1527 0.1990 0.1522 907908 83.40.1099 0.2156 0.1090 907909 70.10.1099 0.1907 0.1090 907910 43.60.1519 0.1400 0.1510 910911 77.90.1408 0.3459 0.1400 910913 77.50.1407 0.3356 0.1400 911912 80.80.1084 0.2512 0.1080 911915 74.90.1405 0.2010 0.1400 913914 81.80.1084 0.2760 0.1080 913917 65.80.1404 0.1278 0.1400 915916 81.70.1082 0.2186 0.1080 915919 41.00.1402 0.1786 0.1400 917918 82.90.1082 0.2569 0.1080 917919 32.70.1402 0.1652 0.1400 919920 82.30.1082 0.1984 0.1080 Constraint error in algorithm Lincs at step 0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.38010e+034.15026e+018.53343e+021.45562e+034.52843e+03 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.78128e+05 -3.41925e+05
