Nvt step gromacs

User discussions
1

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)

2

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

3

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

4

Hi Hanuman,

Did you find a solution for this problem?

5

Yes I did solve this and procceed for the analysis.

Thanks

6

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.

7

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.

8

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?