# Bonds that rotated more than 30 degrees: **URL:** \ **Category:** pmx\ **Created:** [October 14, 2022, 2:21am UTC](https://ask.bioexcel.eu/t/bonds-that-rotated-more-than-30-degrees/3944 "2022-10-14T02:21:48Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![yang1](https://avatars.discourse-cdn.com/v4/letter/y/bc8723/32.png) [@yang1](https://ask.bioexcel.eu/u/yang1)\ **Post date:** [October 14, 2022, 2:21am UTC](https://ask.bioexcel.eu/t/bonds-that-rotated-more-than-30-degrees/3944/1 "2022-10-14T02:21:48Z")
hi , all when I have using the pmx run the moleculer dynamics, I have some trouble in my process. I have done the NVT and NPT , when I have begain my production steps, the wrong have appeared. Step 27126, time 54.252 (ps) LINCS WARNING relative constraint deviation after LINCS: rms -nan, max 1.032528 (between atoms 12023 and 12024) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12017 12018 31.0 0.1229 0.1481 0.1229 12017 12019 67.4 0.1335 0.2312 0.1335 12019 12020 69.9 0.1010 0.1549 0.1010 12023 12024 88.3 0.1090 0.2215 0.1090 12023 12025 88.3 0.1090 0.2208 0.1090 12023 12026 74.9 0.1410 0.2601 0.1410 12026 12027 35.6 0.0960 0.1172 0.0960 12040 12041 53.8 0.1080 0.1449 0.1080 12040 12042 53.7 0.1409 0.2047 0.1409 12042 12045 54.9 0.1409 0.2068 0.1409 12045 12046 54.0 0.1080 0.1446 0.1080 12064 12065 85.6 0.1090 0.1862 0.1090 12064 12066 64.7 0.1526 0.2483 0.1526 12064 12080 64.9 0.1522 0.2515 0.1522 12066 12067 39.2 0.1090 0.1409 0.1090 12066 12068 39.9 0.1090 0.1418 0.1090 12066 12069 32.4 0.1510 0.1813 0.1510 12080 12081 31.1 0.1229 0.1499 0.1229 12080 12082 31.5 0.1335 0.1641 0.1335 Wrote pdb files with previous and current coordinates. what should I do to deal with it ? modify the mdp files ? Which one should I modified? thank you for your answer ? Fr: yang ---
**Author:** ![vgapsys](https://avatars.discourse-cdn.com/v4/letter/v/7993a0/32.png) [@vgapsys](https://ask.bioexcel.eu/u/vgapsys)\ **Post date:** [November 3, 2022, 1:31pm UTC](https://ask.bioexcel.eu/t/bonds-that-rotated-more-than-30-degrees/3944/2 "2022-11-03T13:31:37Z")
The system seems to be unstable. Are you running an alchemical transition? Or is it an equilibrium run? Is the free energy turned on? Are you mutating an amino acid, nucleic acid or a ligand?