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