[gmx-users] linc warnings
subarna thakur
thakur.subarna at yahoo.co.in
Tue Dec 29 12:28:22 CET 2009
Hi
My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message:
Steepest Descents converged to Fmax < 2000 in 372 steps
Potential Energy = -4.1580605e+06
Maximum force = 1.7402682e+03 on atom 820
Norm of force = 3.0794989e+01
-----------------
But during the position restraining step, following Linc warning is coming before stopping all-together
Step 228, time 0.456 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 51159085.131913, max 1100381184.000000 (between atoms 5437 and 5444)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1262 1264 38.8 0.1009 0.1054 0.1000
1262 1263 83.6 0.1035 0.0960 0.1000
1261 1265 42.1 0.1349 0.1366 0.1340
1259 1261 42.9 0.1359 0.1372 0.1340
1237 1241 33.0 0.1480 0.1788 0.1470
1235 1237 75.6 0.1360 0.4797 0.1330
1235 1236 40.9 0.1254 0.3422 0.1230
1232 1233 71.3 0.1834 0.3421 0.1830
1231 1232 43.1 0.1559 0.3294 0.1530
1230 1235 106.0 0.1589 0.2070 0.1530
1230 1231 111.0 0.1606 0.3819 0.1530
1228 1230 81.9 0.1535 8.3688 0.1470
1228 1229 100.8 0.1040 7.2523 0.1000
1226 1228 108.7 0.1480 29.6051 0.1330
1226 1227 112.0 0.1271 25.3002 0.1230
1224 1226 67.7 0.2210 50.5775 0.1530
1224 1225 73.6 0.2217 43.8606 0.1530
1222 1224 146.5 3.0118 273.3403 0.1470
1222 1223 173.1 5.0766 350.6593 0.1000
1220 1222 140.6 50.1464 1239.3472 0.1330
1220 1221 142.5 50.5481 1210.8007 0.1230
1218 1219 46.5 0.1089 0.0687 0.1090
1216 1218 106.3 0.1532 2.4558 0.1390
1216 1217 57.3 0.1434 2.4980 0.1090
1214 1218 106.4 0.1028 2.6673 0.1390
1214 1215 166.4 0.2538 2.1798 0.1090
1212 1216 119.0 0.5844 15.3761 0.1390
1212 1213 50.7 0.5406 17..8588 0.1090
1210 1214 116.2 0.9490 16.1642 0.1390
1210 1211 150.4 0.7387 23.8303 0.1090
1209 1212 57.4 4.3532 165.6521 0.1390
1209 1210 53.5 4.3615 166.9433 0.1390
1208 1209 130.9 34.7441 858.7278 0.1530
1207 1220 174.9 199.1050 3552.6362 0.1530
1207 1208 172.1 195.9491 3367.8894 0.1530
1205 1207 176.1 490.9904 5776.2954 0.1470
1205 1206 177.8 631.7326 5326.1118 0.1000
1203 1205 179.0 1242.0747 9168.7764 0.1330
1203 1204 178.9 1057.3107 7388.7915 0.1230
1202 1203 179.3 1221.3862 8532.1836 0.1530
1200 1202 177.8 455.7037 3702.9392 0.1470
1200 1201 172.7 158.7020 1978.1310 0.1000
1198 1200 174.2 160.3432 1536.1411 0.1330
1198 1199 92.0 16.9060 423.7516 0.1230
1197 1198 94.1 16.9010 421.8028 0.1530
1195 1197 99.1 10.3514 9.3388 0.1470
1195 1196 96.2 9.0920 8.6023 0.1000
1193 1195 91.2 21.5753 58.1620 0..1330
1193 1194 89.2 21.1892 62.7649 0.1230
1191 1192 90.1 50.3829 12.4455 0.1330
1190 1191 89.4 13.1419 10.9133 0.1830
1189 1193 114.3 75.7546 37.4387 0.1530
1189 1190 91.1 24.9488 56.3341 0.1530
1187 1189 146.9 53.8226 42.4679 0.1470
1187 1188 139.0 22.0031 100.4932 0.1000
1185 1187 163.3 21.1472 184.6258 0.1330
1185 1186 170.3 61.0351 169.5860 0.1230
1182 1184 153.3 4.0050 30.0847 0.1530
1182 1183 109.9 2.7482 31.3314 0.1530
1181 1185 170.1 69.8200 192.5774 0.1530
1181 1182 129.0 21.4261 109.4787 0.1530
1179 1181 132.8 19.8073 116.5793 0.1470
1179 1180 159.4 2.3810 48.3401 0..1000
1177 1179 175.2 1.4786 53.0837 0.1330
1177 1178 166.4 0.7559 28.5291 0.1230
1174 1176 90.0 0.1801 80.6845 0.1530
1174 1175 99.7 0.2091 19.2129 0.1530
1173 1177 149.1 0.2721 28.0611 0.1530
1173 1174 73.6 0.7968 36.5323 0.1530
1171 1173 87.8 0.8744 115.1496 0.1470
1171 1172 91.2 0.1603 111.8982 0.1000
1169 1171 89.7 0.2456 106.5120 0.1330
1169 1170 90.0 0.1499 17.6986 0.1230
1166 1168 76.1 0.1256 0.4912 0.1250
1166 1167 77.8 0.1256 0.4782 0.1250
1165 1166 71.9 0.1546 2.7698 0.1530
1164 1169 83.5 0.1781 17.7449 0.1530
1164 1165 89.3 0.1594 8.0829 0..1530
1162 1164 88.0 0.1531 8.2075 0.1470
1162 1163 75.0 0.1015 0.7203 0.1000
1160 1162 77.5 0.1343 1.0789 0.1330
1160 1161 64.4 0.1236 0.1792 0.1230
1159 1160 71.0 0.1533 0.2053 0.1530
1157 1159 45.2 0.1471 0.2126 0.1470
912 914 32.1 0.1354 0.1615 0.1330
912 913 30.7 0.1256 0.1470 0.1230
908 911 30.7 0.1549 0.1695 0.1530
908 909 34.8 0.1445 0.1757 0.1430
907 912 72.9 0.1626 0.1665 0.1530
907 908 37.4 0.1631 0.2368 0.1530
905 907 128.4 0.1701 0.7031 0.1470
905 906 98.7 0.1228 0.6995 0.1000
903 905 168.5 0.2035 2.3071 0..1330
903 904 162.9 0.2507 2.1657 0.1230
900 902 153.1 5.5440 1.2614 0.1530
899 901 121.4 0.4966 2.0792 0.1530
899 900 55.2 5.1698 2.0128 0.1530
898 903 121.2 0.8906 12.7758 0.1530
898 899 131.1 1.2241 13.3134 0.1530
896 898 179.1 3.9358 42.7759 0.1470
896 897 177.8 4.1988 52.7518 0.1000
894 896 168.8 8.6905 122.9769 0.1330
894 895 166.9 8.1428 109.3695 0.1230
891 893 176.5 6.9211 107.7181 0.1530
891 892 177.2 6.9968 107.7183 0.1530
890 894 174.3 15.2302 197.2106 0.1530
890 891 172.5 15.7163 196.0867 0.1530
888 890 175.3 10.5204 153.8357 0..1470
888 889 161.5 7.9441 71.0562 0.1000
886 888 168.5 8.5584 82.3758 0.1330
886 887 141.3 10.6521 51.9678 0.1230
885 886 149.7 9.4837 100.2013 0.1530
883 885 179.0 31.4739 240.4092 0.1470
883 884 169.8 29.0708 297.3551 0.1000
881 883 178.6 67.0574 627.9330 0.1330
881 882 177.3 63.6199 542.5975 0.1230
878 880 116.7 0.1027 0.0457 0.1000
878 879 125.3 0.1034 0.0518 0.1000
874 875 54.5 0.1405 0.2361 0.1340
872 874 113.7 0.1645 3.6744 0.1340
872 873 79.6 0.1285 3.5727 0.1000
871 872 171.5 0.4477 9.9180 0.1470
870 871 165.1 0.5577 29.9169 0..1530
869 870 131.4 4.9544 116.7184 0.1530
868 881 177.7 69.4833 780.9811 0.1530
868 869 176.2 28.7530 434.2484 0.1530
866 868 175.1 25.9538 421.9843 0.1470
866 867 144.2 6.0282 101.1944 0.1000
864 866 89.2 6.6929 141.2832 0.1330
864 865 90.0 0.9032 1979.5164 0.1230
863 864 85.6 0.9540 803.1605 0.1530
861 863 89.8 0.1295 1680.5269 0.1470
861 862 90.8 0.1345 1746.5291 0.1000
859 861 90.4 0.1873 1751.9543 0.1330
859 860 90.1 0.1721 228.2115 0.1230
857 859 90.4 0.1720 227.7394 0.1530
857 858 89.0 0.1739 5.1833 0.1530
855 857 94.2 0.3414 6.0932 0.1470
855 856 55.1 0.3181 1.0624 0.1000
853 855 129.9 1.2924 2.6952 0.1330
853 854 168.7 1.2416 2.1300 0.1230
851 852 102.8 0.5865 0.7272 0.1330
850 851 60.2 0.2345 1.6205 0.1830
849 853 134.8 0.6425 4.7273 0.1530
849 850 157.9 1.9388 2.3807 0.1530
847 849 141.8 0.4117 3.3547 0.1470
847 848 144.2 0.8325 1.2734 0.1000
845 847 139.0 1.3097 1.0164 0.1330
845 846 79.8 0.1358 1.4231 0.1230
844 845 79.5 0.0650 1.5120 0.1530
842 844 44.8 0.2060 0.1625 0.1470
842 843 63.7 0.1102 0.0636 0.1000
840 842 51.6 0.1364 0.1307 0.1330
840 841 62.7 0.1383 0.1741 0.1230
836 840 35.5 0.1762 0.2154 0.1530
532 533 90.0 0.1780 2.1529 0.1780
531 532 75.3 0.1830 0.2559 0..1830
530 531 38.7 0.1530 0.1917 0.1530
5437 5442 178.3 4026489.2500 250662624.0000 0.2282
5440 5443 178.7 3964431.5000 249299120.0000 0.2282
5440 5442 178.2 3994952.7500 249857472.0000 0.2282
5440 5441 177.3 3936231.2500 248309376.0000 0.2282
5439 5444 179.3 4022623.7500 250297056.0000 0.2282
5439 5442 178.7 4005645.5000 249961632.0000 0.2282
5439 5441 177.3 3961649.0000 248898240.0000 0.2282
5438 5444 178.7 4021588.0000 250444048.0000 0.2282
5438 5443 178.4 3977419.0000 249590528.0000 0.2282
5438 5441 177.3 3944925.5000 248506944.0000 0.2282
5437 5444 178.6 4045353.0000 251062960.0000 0.2282
5437 5443 177.7 4017448.2500 250710016.0000 0.2282
t = 0.456 ps: Water molecule starting at atom 154344 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
----------------------------------------------
the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms..
Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings?
Subarna
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