[gmx-users] Regarding error after equilibration of protein in membrane using g_membed
shalini.s at iitg.ernet.in
shalini.s at iitg.ernet.in
Thu Feb 20 14:47:16 CET 2014
Hello...
Thanks justin....I have used POPC 128 for embedding protein. While
embedding the protein using g_membed, it was found that 123 lipids are
overlapping the protein and 10 of them are deleted. Should I use POPC 256
for simulation. Or should i try placing the protein in differently in
POPC128a itself. Kindly suggest. What should I do to place the protein
symmetrically in membrane.
Thanks
Shalini
>
>
> On 2/20/14, 7:44 AM, shalini.s at iitg.ernet.in wrote:
>>
>>
>>
>>
>>
>> ---------------------------- Original Message
>> ----------------------------
>>
>> Hello everyone,
>>
>> I was trying to simulate a protein with POPC membrane. Initially I
>> embedded the protein using InflateGro. But I found that the protein is
>> coming out of the membrane after energy minimization. Then I tried
>
> If that's happening, it means you didn't position the protein correctly or
> the
> box is of insufficient size to accommodate the system. Large movements
> during
> EM should not happen.
>
>> embedding the protein using g_membed. I have successfully created the
>> membedded.gro file. But I am unable to perform the equilibration of
>> membedded.gro. The following error is coming:
>>
>> 3362 3363 177.6 79.3930 763.1334 0.1000
>> 3315 3317 34.1 0.1473 0.1752 0.1470
>> 3323 3325 30.4 0.1383 17.5395 0.1470
>> 3323 3324 125.3 0.1025 3.2656 0.1000
>> 3325 3338 151.8 0.0795 79.4458 0.1530
>> 3325 3326 71.7 0.1390 15.3016 0.1530
>> 3326 3327 156.2 0.1581 1.1020 0.1530
>> 3327 3330 54.1 0.1391 0.2455 0.1390
>> 3327 3328 52.1 0.1390 0.2461 0.1390
>> 3328 3329 36.5 0.1095 0.1503 0.1090
>> 3330 3331 36.7 0.1095 0.1503 0.1090
>> 3317 3321 46.4 0.1534 0.4786 0.1530
>> 3317 3318 33.7 0.1532 0.1795 0.1530
>> 58 60 58.0 0.1538 0.2040 0.1530
>> 58 59 64.0 0.1538 0.1839 0.1530
>> 56 61 40.5 0.1830 6.3293 0.1530
>> 57 58 133.9 0.1615 0.8789 0.1530
>> 3367 3368 161.8 0.6755 12.2433 0.1470
>> 3368 3370 68.0 0.1407 2.3025 0.1340
>> 3368 3369 73.5 0.1046 2.2549 0.1000
>> 3370 3374 109.9 0.1390 0.1579 0.1340
>> 3370 3371 113.2 0.1390 0.1716 0.1340
>> 3371 3373 32.7 0.1020 0.1239 0.1000
>> 3371 3372 36.7 0.1019 0.1287 0.1000
>> 3374 3376 36.9 0.1020 0.0890 0.1000
>> 3374 3375 32.5 0.1020 0.1040 0.1000
>> 3344 3346 145.2 1.4090 50.3186 0.1250
>> 3344 3345 141.0 1.1783 49.6550 0.1250
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>>
>> Step 8, time 0.016 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms nan, max 8994748.000000 (between atoms 3467 and 3473)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>> Step 8, time 0.016 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms nan, max 9896299.000000 (between atoms 3473 and 3475)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 1027 1029 80.0 0.1628 0.4962 0.1530
>> 1029 1031 91.6 0.1905 94.7225 0.1330
>> 1029 1030 52.4 0.1287 0.5485 0.1230
>> 1034 1035 145.5 0.3021 118.3949 0.1430
>> 1035 1036 173.4 0.1196 20.7800 0.1000
>> 1067 1068 176.7 6396.4849 70276.0625 0.1530
>> 1097 1101 70.9 0.1558 0.1831 0.1530
>> 1097 1098 50.7 0.1557 0.2183 0.1530
>> 1098 1099 39.0 0.1435 0.1854 0.1430
>> 1043 1045 158.4 11.4145 1041.2142 0.1530
>> 1043 1044 150.0 11.9767 1018.3463 0.1530
>> 1042 1043 157.3 81.1932 3922.5566 0.1530
>> 1041 1042 163.9 500.7729 14738.6416 0.1530
>> 1041 1046 171.8 1984.2490 40043.3125 0.1530
>> 1046 1048 175.5 5699.0430 88511.3906 0.1330
>> 1048 1050 178.5 12653.2900 165113.2812 0.1470
>> 1048 1049 174.3 5127.7061 74541.0234 0.1000
>> 1046 1047 169.5 1938.5477 35866.9961 0.1230
>> 1039 1041 165.4 553.3626 15883.6680 0.1470
>> 1039 1040 164.8 156.1187 5462.1333 0.1000
>> 1037 1039 167.3 161.4083 6334.0361 0.1330
>> 1037 1038 175.0 32.8745 2147.0396 0.1230
>> 1033 1037 178.0 33.8587 2314.0547 0.1530
>> 1059 1062 179.5 18192.7480 184929.7969 0.1530
>> 1059 1060 179.5 19682.1738 199918.0312 0.1430
>> 1058 1059 179.8 38061.2305 389832.3438 0.1530
>> 1058 1063 179.9 41080.1953 421760.1250 0.1530
>> 1063 1065 179.5 28743.8848 295256.3750 0.1330
>> 1065 1067 178.4 15112.5137 157087.1250 0.1470
>> 1067 1068 176.7 6396.4849 70275.3828 0.1530
>> 1065 1066 178.6 13732.9023 141496.9062 0.1000
>> 1063 1064 179.9 21944.2773 224613.9531 0.1230
>> 1056 1058 179.6 42098.2578 438310.9688 0.1470
>> 1056 1057 179.4 23186.8711 244949.2344 0.1000
>> 1054 1056 179.5 32193.0605 348201.0625 0.1330
>> 1054 1055 179.5 16681.6074 186207.7344 0.1230
>> 1050 1054 179.8 21997.8457 255559.5781 0.1530
>> 1050 1051 178.3 11284.8789 140964.5000 0.1530
>> 1060 1061 179.2 6210.7412 62744.3984 0.1000
>> 5 10 110.9 0.1174 17.8747 0.1530
>> 5 6 43.4 0.1868 1.5629 0.1530
>> 10 12 162.3 2.3017 103.0781 0.1330
>> 10 11 56.2 0.1267 18.4563 0.1230
>> 12 14 123.5 14.2793 574.0925 0.1470
>> 12 13 157.6 2.5007 101.4966 0.1000
>> 3462 3463 179.0 57976.3008 544596.3750 0.1530
>> 3460 3462 179.5 29468.2363 289129.9375 0.1470
>> 3460 3461 179.2 15515.4033 158484.0469 0.1000
>> 3458 3460 179.1 20179.9004 216659.5312 0.1330
>> 3458 3459 176.6 9710.3457 111865.1562 0.1230
>> 3445 3458 177.3 12274.0576 149430.5625 0.1530
>> 3445 3446 175.4 5986.4189 81868.4609 0.1530
>> 3446 3447 175.6 1848.8452 32572.3730 0.1530
>> 3443 3445 176.2 6665.1924 94347.3594 0.1470
>> 3443 3444 175.1 2617.4136 42156.6680 0.1000
>> 3441 3443 177.0 2632.1467 50245.8086 0.1330
>> 3463 3465 179.2 100854.7891 947158.1875 0.1330
>> 3465 3466 179.4 74501.7266 701170.6250 0.1000
>> 3463 3464 178.9 50893.6914 475254.0938 0.1230
>> 3467 3473 179.7 140408.7969 1376196.6250 0.1530
>> 3473 3475 179.4 127823.6641 1316208.0000 0.1330
>> 3475 3477 179.4 109150.6953 1209357.2500 0.1470
>> 3477 3481 179.6 78461.1172 941650.9375 0.1530
>> 3481 3483 177.9 41333.9180 557222.4375 0.1330
>> 3481 3482 178.0 35605.7109 452049.5000 0.1230
>> 3477 3478 178.6 76138.2812 894345.6875 0.1530
>> 3478 3480 176.2 32675.0918 392159.9375 0.1530
>> 3478 3479 176.2 32674.0645 392159.0312 0.1530
>> 3475 3476 179.3 73778.1953 785029.7500 0.1000
>> 3473 3474 179.5 84750.7969 846624.1250 0.1230
>> 3467 3468 180.0 98420.0391 944666.1875 0.1530
>> 3465 3467 179.7 132011.9062 1257875.7500 0.1470
>> 3468 3469 179.4 36424.3828 347810.3438 0.1530
>> 3469 3470 177.6 16064.8076 153743.5781 0.1530
>> 3470 3472 175.5 7414.1357 70933.7031 0.1250
>> 3452 3456 161.6 23.6013 2530.1206 0.1390
>> 3470 3471 175.5 7414.1748 70933.7344 0.1250
>> 3452 3453 159.5 25.5191 1941.0496 0.1090
>> 1031 1033 160.1 3.9653 631.3775 0.1470
>> 1031 1032 86.3 0.1729 94.8543 0.1000
>> 1033 1037 178.0 33.8587 2314.4607 0.1530
>> 1033 1034 157.1 4.4387 632.1960 0.1530
>> 1037 1039 167.3 161.4083 6334.2974 0.1330
>> 1037 1038 175.0 32.8745 2147.2664 0.1230
>> 3487 3489 160.2 263.7160 7937.4644 0.1250
>> 3487 3488 160.7 263.7553 7944.6855 0.1250
>> 3501 3505 117.4 0.2163 29.6946 0.1530
>> 3501 3502 147.6 0.2052 32.6676 0.1530
>> 3502 3503 87.3 0.1781 4.8124 0.1530
>> 1039 1041 165.4 553.3626 15883.7725 0.1470
>> 1039 1040 164.8 156.1187 5462.2422 0.1000
>> 1041 1046 171.8 1984.2490 40043.3555 0.1530
>> 1041 1042 163.9 500.7729 14738.6748 0.1530
>> 1042 1043 157.3 81.1932 3922.5630 0.1530
>> 1043 1045 158.4 11.4145 1041.2142 0.1530
>> 1043 1044 150.0 11.9767 1018.3463 0.1530
>> 1046 1048 175.5 5699.0430 88511.4609 0.1330
>> 1046 1047 169.5 1938.5477 35867.0195 0.1230
>> 1048 1050 178.5 12653.2900 165113.4062 0.1470
>> 1048 1049 174.3 5127.7061 74541.0781 0.1000
>> 1050 1054 179.8 21997.8457 255559.7188 0.1530
>> 1050 1051 178.3 11284.8789 140964.7188 0.1530
>> 1051 1052 174.5 3351.2991 45856.9570 0.1430
>> 1052 1053 164.1 746.5988 13207.4111 0.1000
>> 1054 1056 179.5 32193.0605 348201.1562 0.1330
>> 1054 1055 179.5 16681.6074 186207.8125 0.1230
>> 1056 1058 179.6 42098.2578 438311.0312 0.1470
>> 1056 1057 179.4 23186.8711 244949.2812 0.1000
>> 1058 1063 179.9 41080.1953 421760.1875 0.1530
>> 1058 1059 179.8 38061.2305 389832.3438 0.1530
>> 1059 1060 179.5 19682.1738 199918.0312 0.1430
>> 1060 1061 179.2 6210.7412 62744.3984 0.1000
>> 1063 1065 179.5 28743.8848 295256.5000 0.1330
>> 1063 1064 179.9 21944.2773 224613.9844 0.1230
>> 1065 1067 178.4 15112.5137 157087.4219 0.1470
>> 1065 1066 178.6 13732.9023 141497.0156 0.1000
>> 1068 1070 175.2 3899.3704 46362.0312 0.1330
>> 1068 1069 173.9 3041.7986 35047.2266 0.1230
>> 1070 1072 176.7 2209.7039 29935.6465 0.1470
>> 1070 1071 175.2 1805.4487 22837.9414 0.1000
>> 1072 1076 179.2 922.0685 16932.0977 0.1530
>> 1072 1073 178.6 913.7020 15066.3232 0.1530
>> 1073 1074 173.2 182.1127 4437.1553 0.1430
>> 1074 1075 132.7 24.2450 958.6939 0.1000
>> 1076 1078 175.3 196.7536 7044.7427 0.1330
>> 1076 1077 171.5 196.8930 6733.8765 0.1230
>> 1078 1080 143.8 23.0839 1846.8142 0.1470
>> 1078 1079 148.5 22.6830 1877.4191 0.1000
>> 1080 1093 142.9 2.7365 363.2511 0.1530
>> 1080 1081 138.2 3.1999 357.6469 0.1530
>> 1081 1082 164.8 0.3845 62.1375 0.1530
>> 1082 1085 143.8 0.1653 11.1776 0.1390
>> 1082 1083 100.9 0.1656 10.2468 0.1390
>> 1083 1084 67.5 0.1184 0.2686 0.1090
>> 1093 1095 119.1 0.0851 51.1741 0.1330
>> 1093 1094 80.1 0.0821 49.3375 0.1230
>> 1095 1097 103.4 0.1581 4.6150 0.1470
>> 1059 1062 179.5 18192.7480 184929.7969 0.1530
>> 1085 1086 68.5 0.1189 1.4311 0.1090
>> 1089 1091 109.5 0.1436 0.1671 0.1390
>> 1089 1090 137.4 0.1127 0.2066 0.1090
>> 1091 1092 30.4 0.1109 0.1406 0.1090
>> 1 2 157.9 0.1045 0.3246 0.1000
>> 1 4 88.0 0.1042 0.2268 0.1000
>> 1 3 115.5 0.1042 0.2331 0.1000
>> 14 18 172.4 92.4183 2767.2874 0.1530
>> 14 15 122.5 13.9933 575.6103 0.1530
>> 18 20 178.6 419.3188 6866.1240 0.1330
>> 18 19 171.3 98.4866 2755.2510 0.1230
>> 20 22 179.0 964.6424 12122.3223 0.1470
>> 20 21 177.8 408.7984 5702.4966 0.1000
>> 22 26 178.9 1536.1716 17321.9004 0.1530
>> 22 23 179.1 836.6511 10026.1953 0.1530
>> 23 24 179.3 254.7649 3362.1853 0.1430
>> 24 25 174.0 52.1336 1016.7377 0.1000
>> 26 28 179.4 2084.2344 22023.2852 0.1330
>> 26 27 178.5 1120.8782 12176.0635 0.1230
>> 28 30 179.5 2588.0381 26462.7246 0.1470
>> 28 29 179.6 1465.2933 15128.7061 0.1000
>> 30 34 178.9 2794.1572 28349.2109 0.1530
>> 34 36 179.6 2646.0776 27351.9727 0.1330
>> 36 40 179.0 1673.8123 17524.4531 0.1470
>> 39 40 175.4 442.7062 4523.2490 0.1530
>> 38 39 175.8 268.5752 3065.6282 0.1530
>> 36 37 179.5 2280.8997 24410.9434 0.1470
>> 37 41 179.7 1703.3684 19312.5781 0.1530
>> 41 43 179.5 1104.6077 13765.5645 0.1330
>> 41 42 179.5 852.7722 10117.8877 0.1230
>> 37 38 179.5 1311.9948 14467.6621 0.1530
>> 34 35 178.7 1714.1815 17439.5176 0.1230
>> 30 31 178.9 1909.6912 19281.2168 0.1530
>> 15 16 153.8 1.9236 77.6755 0.1430
>> 16 17 86.5 0.1081 11.4437 0.1000
>> 3353 3354 172.4 129.3383 1310.9741 0.1530
>> 3352 3353 175.0 386.0269 3753.5488 0.1530
>> 3351 3352 177.9 1113.5554 10680.0088 0.1530
>> 3351 3360 178.9 1572.3097 15148.9863 0.1530
>> 3360 3362 178.9 1364.4799 13459.5615 0.1330
>> 3362 3364 178.6 1058.5470 11095.3564 0.1470
>> 3362 3363 178.3 763.1334 7694.2603 0.1000
>> 3360 3361 179.0 934.6445 9024.5508 0.1230
>> 3349 3351 179.1 1552.0356 14997.7021 0.1470
>> 3349 3350 179.0 911.5491 8850.9189 0.1000
>> 3347 3349 179.1 1319.2100 13121.4463 0.1330
>> 3347 3348 178.4 732.0328 7468.3926 0.1230
>> 3342 3347 178.8 1015.0016 10807.9424 0.1530
>> 3354 3355 173.4 40.0122 478.2587 0.1530
>> 3355 3356 173.3 12.1603 252.2795 0.1470
>> 3356 3359 172.8 2.3791 145.9443 0.1000
>> 3356 3358 171.2 2.3763 145.7469 0.1000
>> 3356 3357 173.7 2.6682 146.0062 0.1000
>> 3403 3405 103.6 0.1378 1.2758 0.1330
>> 3403 3404 153.1 0.1278 1.4976 0.1230
>> 3419 3421 131.3 0.1372 0.8668 0.1330
>> 3419 3420 59.4 0.1247 0.1176 0.1230
>> 3421 3423 51.9 0.1703 10.4834 0.1470
>> 3421 3422 122.8 0.1037 0.9254 0.1000
>> 3436 3438 166.3 10.4744 1413.8136 0.1330
>> 3436 3437 114.4 0.3693 237.5648 0.1230
>> 3438 3440 146.1 67.4800 5238.9019 0.1470
>> 3438 3439 166.4 10.5449 1416.5234 0.1000
>> 3440 3441 172.5 531.2781 20227.8926 0.1530
>> 3441 3443 177.0 2632.1467 50246.4805 0.1330
>> 3441 3442 172.4 508.0948 19738.8613 0.1230
>> 3443 3445 176.2 6665.1924 94347.8750 0.1470
>> 3443 3444 175.1 2617.4136 42157.0195 0.1000
>> 3445 3458 177.3 12274.0576 149430.8594 0.1530
>> 3445 3446 175.4 5986.4189 81868.9766 0.1530
>> 3446 3447 175.6 1848.8452 32573.3789 0.1530
>> 3447 3450 174.4 552.9905 16398.2070 0.1390
>> 3447 3448 174.5 521.7374 15794.0234 0.1390
>> 3448 3452 165.5 117.3935 6163.6240 0.1390
>> 3448 3449 164.5 114.2863 5485.2617 0.1090
>> 3450 3454 170.3 149.6735 7179.2744 0.1390
>> 3450 3451 170.3 146.7532 6152.4673 0.1090
>> 3458 3460 179.1 20179.9004 216659.6094 0.1330
>> 3458 3459 176.6 9710.3457 111865.2422 0.1230
>> 3460 3462 179.5 29468.2363 289129.9375 0.1470
>> 3462 3463 179.0 57976.3008 544596.3750 0.1530
>> 3463 3464 178.9 50893.6914 475254.0938 0.1230
>> 3460 3461 179.2 15515.4033 158484.0625 0.1000
>> 3423 3436 104.6 0.4001 233.3529 0.1530
>> 3423 3424 40.9 0.1755 11.1352 0.1530
>> 3424 3425 157.5 0.1562 1.2625 0.1530
>> 3425 3428 53.6 0.1398 0.2414 0.1390
>> 3425 3426 58.3 0.1398 0.2431 0.1390
>> 3426 3430 32.1 0.1392 0.1881 0.1390
>> 3426 3427 39.7 0.1092 0.1600 0.1090
>> 3428 3432 33.2 0.1392 0.1913 0.1390
>> 3428 3429 40.8 0.1092 0.1635 0.1090
>> 3454 3456 170.4 29.3483 2976.2119 0.1390
>> 3454 3455 171.0 27.1603 2467.2502 0.1090
>> 3456 3457 153.1 4.0565 1050.8282 0.1090
>> 3389 3403 52.1 0.1444 12.1950 0.1530
>> 3390 3391 133.1 0.1605 1.9391 0.1530
>> 3391 3394 58.6 0.1399 0.2710 0.1390
>> 3391 3392 54.0 0.1400 0.2720 0.1390
>> 3392 3396 30.4 0.1393 0.1808 0.1390
>> 3392 3393 37.7 0.1093 0.1521 0.1090
>> 3465 3467 179.7 132011.9062 1257875.7500 0.1470
>> 3467 3468 180.0 98420.0391 944666.1875 0.1530
>> 3468 3469 179.4 36424.3828 347810.3438 0.1530
>> 3469 3470 177.6 16064.8076 153743.5781 0.1530
>> 3470 3472 175.5 7414.1357 70933.7031 0.1250
>> 3470 3471 175.5 7414.1748 70933.7344 0.1250
>> 3465 3466 179.4 74501.7266 701170.6250 0.1000
>> 3463 3465 179.2 100854.7891 947158.1875 0.1330
>> 3473 3475 179.4 127823.6641 1316208.0000 0.1330
>> 3473 3474 179.5 84750.7969 846624.1250 0.1230
>> 3467 3473 179.7 140408.7969 1376196.6250 0.1530
>> 3475 3477 179.4 109150.6953 1209357.3750 0.1470
>> 3475 3476 179.3 73778.1953 785029.7500 0.1000
>> 3477 3481 179.6 78461.1172 941651.3750 0.1530
>> 3477 3478 178.6 76138.2812 894345.8125 0.1530
>> 3478 3480 176.2 32675.0918 392160.0000 0.1530
>> 3478 3479 176.2 32674.0645 392159.0625 0.1530
>> 3481 3483 177.9 41333.9180 557223.3125 0.1330
>> 3481 3482 178.0 35605.7109 452049.9062 0.1230
>> 3483 3485 174.7 16345.8555 272683.5625 0.1470
>> 3483 3484 173.0 15823.4551 241226.0156 0.1000
>> 3485 3490 165.9 4770.5640 108365.1797 0.1530
>> 3485 3486 165.2 4518.4497 103572.5938 0.1530
>> 3486 3487 153.2 980.2649 27058.5469 0.1530
>> 3490 3492 162.2 1621.9301 42007.1523 0.1330
>> 3490 3491 158.0 1432.9362 35743.0234 0.1230
>> 3505 3507 96.8 0.1458 2.3278 0.1330
>> 3507 3508 33.7 0.1034 0.1077 0.1000
>> 3495 3496 168.0 104.8195 3996.6477 0.1530
>> 3492 3496 174.1 519.5735 16371.8955 0.1470
>> 3492 3493 174.5 567.5291 18394.0684 0.1470
>> 3493 3497 176.1 167.2048 7566.0293 0.1530
>> 3493 3494 175.3 169.2546 6737.7095 0.1530
>> 3494 3495 171.7 22.7750 734.1775 0.1530
>> 3497 3499 176.7 25.7030 2471.0254 0.1330
>> 3497 3498 175.6 26.1585 2463.9937 0.1230
>> 3499 3501 111.6 0.6449 420.6371 0.1470
>> 3499 3500 102.4 0.7552 411.8347 0.1000
>> 34 36 179.6 2646.0776 27352.0215 0.1330
>> 34 35 178.7 1714.1815 17439.5254 0.1230
>> 30 34 178.9 2794.1572 28349.2070 0.1530
>> 30 31 178.9 1909.6912 19281.2051 0.1530
>> 31 32 178.6 669.4272 6709.6001 0.1430
>> 32 33 177.0 210.3252 2106.0405 0.1000
>> 28 30 179.5 2588.0381 26462.6562 0.1470
>> 28 29 179.6 1465.2933 15128.6387 0.1000
>> 26 28 179.4 2084.2344 22023.0234 0.1330
>> 26 27 178.5 1120.8782 12175.8223 0.1230
>> 22 26 178.9 1536.1716 17321.2539 0.1530
>> 22 23 179.1 836.6511 10025.5244 0.1530
>> 20 22 179.0 964.6424 12121.2207 0.1470
>> 36 40 179.0 1673.8123 17524.5020 0.1470
>> 36 37 179.5 2280.8997 24411.1484 0.1470
>> 37 41 179.7 1703.3684 19313.1484 0.1530
>> 37 38 179.5 1311.9948 14467.8604 0.1530
>> 38 39 175.8 268.5752 3065.6682 0.1530
>> 39 40 175.4 442.7062 4523.2490 0.1530
>> 41 43 179.5 1104.6077 13766.8037 0.1330
>> 41 42 179.5 852.7722 10118.3906 0.1230
>> 43 45 178.0 638.9901 9176.0869 0.1470
>> 43 44 177.3 509.0827 6880.1655 0.1000
>> 31 32 178.6 669.4272 6709.6001 0.1430
>> 45 52 178.7 319.6538 5529.2925 0.1530
>> 45 46 178.2 282.3339 4720.5020 0.1530
>> 46 47 173.8 70.4505 1504.9238 0.1530
>> 32 33 177.0 210.3252 2106.0405 0.1000
>> 47 49 161.3 19.6105 541.3401 0.1330
>> 47 48 156.5 17.9500 489.8326 0.1230
>> 52 54 178.4 121.1273 2809.6111 0.1330
>> 52 53 176.9 115.7046 2369.7856 0.1230
>> 54 56 173.8 30.7841 1199.7819 0.1470
>> 54 55 170.8 28.7333 1070.6758 0.1000
>> 61 63 154.9 0.8056 113.5082 0.1330
>> 61 62 152.6 0.9701 110.9714 0.1230
>> 63 65 114.5 0.1635 18.9735 0.1470
>> 63 64 44.5 0.1199 20.1058 0.1000
>> 49 51 167.0 4.7028 179.1507 0.1000
>> 49 50 166.3 4.1565 178.9935 0.1000
>> 3360 3362 178.9 1364.4799 13460.2031 0.1330
>> 3360 3361 179.0 934.6445 9024.7812 0.1230
>> 3364 3377 179.0 681.2372 7991.8003 0.1530
>> 3364 3365 179.3 592.1429 6585.6948 0.1530
>> 3365 3366 177.1 186.7547 2220.7898 0.1530
>> 3366 3367 167.3 49.4988 694.8265 0.1530
>> 3377 3379 176.6 344.8001 4881.1123 0.1330
>> 3377 3378 175.9 296.5232 3865.3970 0.1230
>> 3379 3381 173.8 141.9351 2754.0537 0.1470
>> 3379 3380 170.3 129.8175 2195.7815 0.1000
>> 3387 3389 127.4 0.5756 92.3510 0.1470
>> 3387 3388 125.7 0.4652 90.9280 0.1000
>> 3405 3407 36.5 0.1484 0.1640 0.1470
>> 3405 3406 51.0 0.1013 0.1236 0.1000
>> 3415 3417 43.4 0.1472 0.2122 0.1470
>> 3417 3419 50.8 0.1545 0.1089 0.1530
>> 3417 3418 42.7 0.1532 0.2148 0.1530
>> 65 78 63.1 0.1601 1.4500 0.1530
>> 65 66 31.5 0.1599 1.6286 0.1530
>> 66 67 79.5 0.1539 0.0396 0.1530
>> 3381 3385 178.0 39.7059 1328.7585 0.1530
>> 3381 3382 176.8 40.0948 1266.3851 0.1530
>> 3382 3384 156.5 9.5596 382.9987 0.1530
>> 3382 3383 155.7 9.5266 382.1747 0.1530
>> 3385 3387 166.5 6.6590 461.6463 0.1330
>> 3385 3386 167.1 6.8378 457.0848 0.1230
>> 3321 3323 162.9 3.3125 321.9170 0.1330
>> 3321 3322 148.4 0.4733 75.7302 0.1230
>> 3338 3340 178.8 298.4420 4798.5874 0.1330
>> 3338 3339 175.7 67.5963 2081.7659 0.1230
>> 3340 3342 178.8 659.4686 7905.7197 0.1470
>> 3340 3341 178.7 286.3703 3826.8704 0.1000
>> 3342 3347 178.8 1015.0016 10809.3057 0.1530
>> 3342 3343 178.6 567.7331 6502.3530 0.1530
>> 3343 3344 178.1 181.9402 2496.5640 0.1530
>> 3347 3349 179.1 1319.2100 13122.1016 0.1330
>> 3347 3348 178.4 732.0328 7468.9658 0.1230
>> 3349 3351 179.1 1552.0356 14997.9990 0.1470
>> 3349 3350 179.0 911.5491 8851.1504 0.1000
>> 3351 3360 178.9 1572.3097 15149.2822 0.1530
>> 3351 3352 177.9 1113.5554 10680.1240 0.1530
>> 3352 3353 175.0 386.0269 3753.5671 0.1530
>> 3353 3354 172.4 129.3383 1310.9741 0.1530
>> 3354 3355 173.4 40.0122 478.2587 0.1530
>> 3355 3356 173.3 12.1603 252.2795 0.1470
>> 3356 3359 172.8 2.3791 145.9443 0.1000
>> 3356 3358 171.2 2.3763 145.7469 0.1000
>> 3356 3357 173.7 2.6682 146.0062 0.1000
>> 3362 3364 178.6 1058.5470 11096.6514 0.1470
>> 3362 3363 178.3 763.1334 7694.8149 0.1000
>> 3394 3395 37.3 0.1093 0.1508 0.1090
>> 3313 3315 116.4 0.1392 0.5993 0.1330
>> 3313 3314 37.3 0.1250 0.1475 0.1230
>> 3315 3317 70.8 0.1752 12.2839 0.1470
>> 3315 3316 136.3 0.1060 0.6688 0.1000
>> 3323 3325 169.7 17.5395 1003.5385 0.1470
>> 3323 3324 167.2 3.2656 313.7166 0.1000
>> 3325 3338 177.2 79.4458 2416.8191 0.1530
>> 3325 3326 164.7 15.3016 890.7102 0.1530
>> 3326 3327 128.9 1.1020 179.7763 0.1530
>> 3327 3330 172.4 0.2455 35.6724 0.1390
>> 3327 3328 169.0 0.2461 35.4509 0.1390
>> 3328 3329 64.5 0.1503 6.5250 0.1090
>> 3330 3331 67.7 0.1503 6.5282 0.1090
>> 3332 3336 99.4 0.1531 1.1767 0.1390
>> 3332 3333 163.8 0.1220 1.3145 0.1090
>> 3334 3336 99.2 0.1530 1.1729 0.1390
>> 3334 3335 163.4 0.1218 1.3080 0.1090
>> 3317 3321 156.6 0.4786 78.9164 0.1530
>> 3317 3318 40.1 0.1795 13.4933 0.1530
>> 3318 3320 88.8 0.1566 1.6192 0.1530
>> 3318 3319 157.6 0.1566 1.8334 0.1530
>> 58 60 118.9 0.2040 14.8632 0.1530
>> 58 59 129.2 0.1839 15.2533 0.1530
>> 56 61 167.7 6.3293 429.3639 0.1530
>> 56 57 161.0 6.6174 401.0884 0.1530
>> 57 58 157.7 0.8789 88.1074 0.1530
>> 3367 3368 159.4 12.2433 217.5954 0.1470
>> 3368 3370 169.3 2.3025 81.3744 0.1340
>> 3368 3369 166.9 2.2549 80.3822 0.1000
>> 3370 3374 116.5 0.1579 16.4463 0.1340
>> 3370 3371 127.4 0.1716 16.9143 0.1340
>> 3371 3373 140.3 0.1239 2.2868 0.1000
>> 3371 3372 94.2 0.1287 2.1349 0.1000
>> 3374 3376 129.5 0.0890 1.5141 0.1000
>> 3374 3375 83.4 0.1040 1.4698 0.1000
>> 3344 3346 167.4 50.3186 1002.2032 0.1250
>> 3344 3345 167.3 49.6550 1002.0633 0.1250
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.5.5
>> Source code file: constr.c, line: 189
>>
>> Fatal error:
>> Too many LINCS warnings (1064)
>> If you know what you are doing you can adjust the lincs warning
>> threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>
> I have never had much success with g_membed; the configurations it
> generates
> usually have bad clashes. I suppose there are ways around this by
> "softening"
> interactions, e.g. using the free energy code or some other trick, but
> your
> results clearly indicate the system is unstable. Perhaps you need more
> thorough
> energy minimization.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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Shalini Singh
Research Scholar
Department of Biotechnology
IIT Guwahati
Guwahati
Assam-781039
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