# Nvt step gromacs **URL:** \ **Category:** User discussions\ **Created:** [January 18, 2021, 1:56pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462 "2021-01-18T13:56:33Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\ **Post date:** [January 18, 2021, 1:56pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/1 "2021-01-18T13:56:33Z")
Please help me to fix the following error. I am trying to fix it from one month Command line: gmx mdrun -deffnm 06\_nvt Reading file 06\_nvt.tpr, VERSION 2020 (single precision) Changing nstlist from 10 to 100, rlist from 1.4 to 1.537 1 GPU selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node: PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 16 OpenMP threads Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.012422, max 0.320517 (between atoms 221 and 230) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025920, max 1.186125 (between atoms 8538 and 8540) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 232 234 32.9 0.1913 0.2004 0.1470 234 240 37.9 0.1966 0.1976 0.1530 240 242 39.1 0.1708 0.1941 0.1330 242 244 38.6 0.1779 0.1802 0.1470 8536 8538 46.5 0.1586 0.1172 0.1330 8538 8540 30.4 0.1926 0.3214 0.1470 8540 8541 70.2 0.1591 0.0953 0.1530 8540 8547 111.5 0.1770 0.0608 0.1530 Wrote pdb files with previous and current coordinates starting mdrun ‘NSP12’ 100000 steps, 200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.057034, max 1.997822 (between atoms 8538 and 8540) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 217 219 32.9 0.1661 0.0509 0.1330 219 220 38.8 0.1055 0.1026 0.1000 221 230 49.6 0.2020 0.0674 0.1530 230 231 31.8 0.1278 0.1204 0.1230 232 233 43.1 0.1033 0.1135 0.1000 232 234 62.8 0.1913 0.0678 0.1470 240 242 71.4 0.1708 0.0709 0.1330 242 243 38.9 0.1062 0.1380 0.1000 244 245 52.9 0.1711 0.0576 0.1530 244 249 45.2 0.1720 0.0541 0.1530 8527 8528 30.1 0.1343 0.1676 0.1230 8527 8529 74.0 0.1634 0.0419 0.1330 8529 8530 50.4 0.1051 0.0866 0.1000 8538 8539 86.2 0.1072 0.0734 0.1000 8538 8540 36.0 0.1926 0.4407 0.1470 8540 8541 144.5 0.1591 0.2447 0.1530 8540 8547 162.2 0.1770 0.3164 0.1530 8544 8545 33.6 0.1032 0.0364 0.1000 8544 8546 93.2 0.0990 0.2041 0.1000 8549 8550 124.0 0.1120 0.0500 0.1000 8549 8551 30.6 0.1768 0.2008 0.1470 8551 8552 51.9 0.1679 0.0829 0.1530 8551 8556 34.7 0.1615 0.0736 0.1530 8618 8619 38.7 0.1090 0.1087 0.1090 Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1# Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.382344, max 19.519989 (between atoms 8540 and 8547) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 195 208 41.5 0.1510 0.0449 0.1530 208 209 42.7 0.1200 0.0474 0.1230 212 217 66.6 0.2945 0.1768 0.1530 217 218 93.7 0.1661 0.1644 0.1230 217 219 58.6 0.0509 0.4572 0.1330 219 220 103.8 0.1026 0.2081 0.1000 219 221 144.4 0.3272 0.2776 0.1470 221 222 124.3 0.2419 0.3013 0.1530 221 230 52.1 0.0674 0.5596 0.1530 230 231 133.4 0.1204 0.1650 0.1230 230 232 67.4 0.2844 0.1237 0.1330 232 233 89.8 0.1135 0.1330 0.1000 232 234 69.4 0.0678 0.2838 0.1470 234 235 47.0 0.2499 0.2287 0.1530 240 241 90.7 0.0898 0.0858 0.1230 240 242 81.3 0.0709 0.2186 0.1330 242 243 82.3 0.1380 0.1904 0.1000 242 244 35.3 0.3190 0.2052 0.1470 244 245 30.2 0.0576 0.1613 0.1530 244 249 78.5 0.0541 0.1356 0.1530 8519 8521 47.5 0.1107 0.0397 0.1470 8527 8528 44.6 0.1676 0.1546 0.1230 8527 8529 78.2 0.0419 0.3047 0.1330 8529 8530 103.6 0.0866 0.2050 0.1000 8529 8531 78.0 0.3196 0.1512 0.1470 8531 8532 136.3 0.2741 0.0859 0.1530 8536 8538 34.4 0.2563 0.7950 0.1330 8538 8539 34.8 0.0734 0.7963 0.1000 8538 8540 171.1 0.4407 1.8610 0.1470 8540 8541 162.9 0.2447 2.1696 0.1530 8540 8547 174.6 0.3164 3.1396 0.1530 8541 8542 166.1 0.1897 0.8762 0.1530 8544 8545 46.0 0.0364 0.0330 0.1000 8544 8546 37.0 0.2041 0.1329 0.1000 8547 8548 173.8 0.2724 1.9430 0.1230 8547 8549 171.8 0.3647 2.0607 0.1330 8549 8550 126.1 0.0500 0.6825 0.1000 8551 8552 32.7 0.0829 0.1423 0.1530 Wrote pdb files with previous and current coordinates Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 483.403198, max 25345.556641 (between atoms 8542 and 8543) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 193 194 94.7 0.0930 0.0183 0.1000 195 208 75.2 0.0449 0.1432 0.1530 196 197 53.1 0.1407 0.0384 0.1530 208 209 32.7 0.0474 0.0997 0.1230 210 211 62.0 0.0872 0.0730 0.1000 210 212 61.9 0.1331 0.0501 0.1470 212 213 98.6 0.1185 0.0407 0.1530 212 217 97.5 0.1768 0.5731 0.1530 217 218 144.1 0.1644 0.3908 0.1230 217 219 152.3 0.4572 0.8276 0.1330 219 220 175.1 0.2081 0.9189 0.1000 219 221 164.0 0.2776 1.5768 0.1470 221 222 157.9 0.3013 1.3927 0.1530 221 230 168.6 0.5596 1.3828 0.1530 222 223 144.4 0.1744 0.5428 0.1530 224 225 31.0 0.1512 0.1545 0.1530 226 227 30.4 0.0998 0.1217 0.1000 226 229 32.0 0.0998 0.1225 0.1000 230 231 162.1 0.1650 0.7034 0.1230 230 232 86.2 0.1237 0.9813 0.1330 232 233 75.5 0.1330 0.1485 0.1000 232 234 57.3 0.2838 0.2141 0.1470 234 240 48.7 0.1456 0.3955 0.1530 240 241 139.0 0.0858 0.2506 0.1230 240 242 102.1 0.2186 0.1875 0.1330 242 243 77.6 0.1904 0.1788 0.1000 242 244 73.7 0.2052 0.1469 0.1470 244 245 39.1 0.1613 0.3191 0.1530 244 249 42.8 0.1356 0.2649 0.1530 245 246 102.8 0.1338 0.0796 0.1430 245 248 100.9 0.1407 0.0927 0.1530 249 250 42.8 0.1296 0.1165 0.1230 251 253 43.8 0.0343 0.0419 0.1470 8519 8520 44.8 0.1006 0.0910 0.1000 8521 8522 53.2 0.0509 0.1388 0.1530 8521 8527 39.8 0.2094 0.1958 0.1530 8527 8528 49.8 0.1546 0.1143 0.1230 8527 8529 36.5 0.3047 0.1672 0.1330 8529 8530 85.6 0.2050 0.1840 0.1000 8529 8531 81.8 0.1512 0.8974 0.1470 8531 8532 31.4 0.0859 1.0595 0.1530 8531 8536 60.3 0.2136 2.8937 0.1530 8536 8537 72.4 0.1360 630.1425 0.1230 8536 8538 150.6 0.7950 4.7104 0.1330 8538 8539 156.2 0.7963 4.1387 0.1000 8538 8540 167.1 1.8610 6.2497 0.1470 8540 8541 168.5 2.1696 7.6262 0.1530 8541 8542 149.4 0.8762 3119.6611 0.1530 8542 8543 163.3 0.5184 3117.6265 0.1230 8542 8544 158.9 0.4723 3117.4692 0.1330 8544 8545 55.3 0.0330 3.5915 0.1000 8544 8546 128.6 0.1329 3.6974 0.1000 8547 8548 43.7 1.9430 2329.2944 0.1230 8547 8549 145.8 2.0607 721.2332 0.1330 8549 8550 131.4 0.6825 722.3632 0.1000 8549 8551 143.0 0.7541 721.7413 0.1470 8551 8552 139.9 0.1423 3.5736 0.1530 8551 8556 117.2 0.1372 3.3278 0.1530 8552 8553 34.0 0.1493 1.0089 0.1430 8552 8555 33.3 0.1547 1.0083 0.1530 8553 8554 146.4 0.1020 0.5365 0.1000 8558 8559 104.6 0.1003 0.2085 0.1000 8558 8560 121.0 0.1473 0.1945 0.1470 step 2: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [January 18, 2021, 4:55pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/2 "2021-01-18T16:55:18Z")
Hi, It looks like your initial structure has same issue. The first warning regards atoms 221 and 230. You can check your structure and in particular atom 221 and 230. Also it is good to energy minimize the system before setting NVT simulation. Best regards Alessandra ---
**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\ **Post date:** [January 19, 2021, 5:51am UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/3 "2021-01-19T05:51:35Z")
Thank you Ma’am for your reply. I did energy minimization but it gives errors like em stopped at 357 steps…How can I rectify the error. What should I do? Your sincerely Hanuman ---
**Author:** ![owusuj](https://avatars.discourse-cdn.com/v4/letter/o/8491ac/32.png) [@owusuj](https://gromacs.bioexcel.eu/u/owusuj)\ **Post date:** [August 2, 2021, 5:05pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/4 "2021-08-02T17:05:43Z")
Hi Hanuman, Did you find a solution for this problem? ---
**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\ **Post date:** [August 2, 2021, 6:03pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/5 "2021-08-02T18:03:44Z")
Yes I did solve this and procceed for the analysis. Thanks ---
**Author:** ![owusuj](https://avatars.discourse-cdn.com/v4/letter/o/8491ac/32.png) [@owusuj](https://gromacs.bioexcel.eu/u/owusuj)\ **Post date:** [August 2, 2021, 6:25pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/6 "2021-08-02T18:25:11Z")
Great. I will be glad if you could share how you solved it. Because I am stuck at this error as well. Even in minimization I am having this Lincs warning. ---
**Author:** ![hanuman](https://avatars.discourse-cdn.com/v4/letter/h/eada6e/32.png) [@hanuman](https://gromacs.bioexcel.eu/u/hanuman)\ **Post date:** [August 2, 2021, 8:58pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/7 "2021-08-02T20:58:03Z")
Please send your errors file on email as my laptop is not working. I will repair it within 4-5 days but by looking at the error I can suggest what to do. ---
**Author:** ![sangita](https://avatars.discourse-cdn.com/v4/letter/s/7993a0/32.png) [@sangita](https://gromacs.bioexcel.eu/u/sangita)\ **Post date:** [April 18, 2023, 9:45pm UTC](https://gromacs.bioexcel.eu/t/nvt-step-gromacs/1462/8 "2023-04-18T21:45:40Z")
Hi Hanuman, I am getting similar error that you got on 2021 Step 18052, time 72.208 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 38.425972, max 7092.694824 (between atoms 33369 and 33370) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 33348 33350 37.5 0.1426 0.2012 0.1430 33350 33351 51.3 0.1077 0.1830 0.1080 33352 33350 36.8 0.1535 0.2107 0.1538 33365 33350 78.1 0.1472 0.2815 0.1490 33366 33365 48.8 0.1218 0.2894 0.1230 33365 33367 170.5 0.1324 0.5061 0.1345 33369 33370 80.5 0.8129 766.1191 0.1080 33371 33369 133.2 0.2047 2.3895 0.1538 33379 33369 154.1 0.1626 1.1798 0.1490 33371 33372 167.1 0.5772 1.2834 0.1111 33371 33373 134.0 0.8306 1.1405 0.1111 33374 33371 165.0 0.1381 1.4058 0.1522 33374 33375 33.8 0.1477 0.3888 0.1230 33376 33377 164.4 0.1052 0.1521 0.1000 33376 33378 99.4 0.1092 0.0634 0.1000 33436 33437 98.9 0.1080 0.0467 0.1080 33438 33436 92.3 0.1500 0.4427 0.1500 33438 33439 92.2 0.1111 0.4702 0.1111 33440 33438 92.1 0.1420 0.4717 0.1420 33442 33438 90.9 0.1538 2.7166 0.1538 33442 33443 90.5 0.1111 2.6912 0.1111 33442 33444 116.4 0.1111 762.0467 0.1111 33442 33445 90.6 0.1111 2.5637 0.1111 Wrote pdb files with previous and current coordinates Could you suggest me how did you solve your problem?