nvt步骤报错了（LINCS WARNING）

jia1012428

当我运行到gmx mdrun -v -deffnm nvt时，有报错了，请问老师怎么解决，nvt文件在附件，谢谢老师
Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.
step 13100, will finish Sat Feb 18 00:53:14 2023
Step 13109, time 26.218 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.215484, max 10.827924 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    0.0973   1.1509      0.0973
Wrote pdb files with previous and current coordinates


Step 13110, time 26.22 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001360, max 0.068317 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    1.1509   0.1039      0.0973


Step 13111, time 26.222 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.211482, max 10.626864 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    0.1039   1.1313      0.0973
Wrote pdb files with previous and current coordinates


Step 13112, time 26.224 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005146, max 0.258576 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    1.1313   0.1225      0.0973


Step 13113, time 26.226 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.217564, max 10.932468 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    0.1225   1.1610      0.0973
Wrote pdb files with previous and current coordinates


Step 13114, time 26.228 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000948, max 0.047660 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   5088   5092   90.0    1.1610   0.1019      0.0973


Step 13115, time 26.23 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.207697, max 10.420547 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
    990    991   90.0    0.1010   0.1595      0.1010
   5088   5092   90.0    0.1019   1.1112      0.0973
Wrote pdb files with previous and current coordinates


Step 13116, time 26.232 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.217311, max 10.673550 (between atoms 982 and 985)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
    982    985   90.0    0.1090   1.2724      0.1090
    990    991   90.0    0.1595   0.3303      0.1010
   5088   5092   90.0    1.1112   0.1363      0.0973
Wrote pdb files with previous and current coordinates


Step 13117, time 26.234 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.227283, max 10.549366 (between atoms 5088 and 5092)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
    982    983   43.6    0.1064   0.1150      0.1090
    982    984   90.0    0.1069   0.1715      0.1090
    982    985   90.0    1.2724   0.4246      0.1090
    990    991   90.0    0.3303   0.4272      0.1010
   3822   3823   41.8    0.1010   0.1010      0.1010
   5088   5092   90.0    0.1363   1.1238      0.0973
Wrote pdb files with previous and current coordinates


Step 13118, time 26.236 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 794092.187500, max 28215452.000000 (between atoms 982 and 985)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
    982    983   90.0    0.1150   0.1336      0.1090
    982    984   43.8    0.1715   0.1059      0.1090
    982    985   40.8    0.4246 3075484.5000      0.1090
    990    991   90.0    0.4272   0.3401      0.1010
   1230   1232   31.7    0.1090   0.1048      0.1090
   1230   1233   90.0    0.1090   1.8879      0.1090
   1288   1289   90.0    0.1090   0.5925      0.1090
   1288   1290   90.0    0.1090   0.5188      0.1090
   1288   1291  110.7    0.1090 3075478.7500      0.1090
   3822   3823   35.6    0.1010   0.1010      0.1010
   5088   5092   90.0    1.1238   0.1254      0.0973
Wrote pdb files with previous and current coordinates

sobereva

老生常谈问题
http://sobereva.com/soft/Sobtop#FAQ8

jia1012428

sobereva 发表于 2023-2-18 09:51
老生常谈问题
http://sobereva.com/soft/Sobtop#FAQ8

老师太专业了，我学学，谢谢！

jia1012428

sobereva 发表于 2023-2-18 09:51
老生常谈问题
http://sobereva.com/soft/Sobtop#FAQ8

您好，我用的是acpype网站生成的配体文件。当我用转氨酶与单配体（pmp或mba）的MD时，两个都没有问题。但是用转氨酶与双配体（pmp或mba）做MD，就会有刚才的报错。能简要说下，我这个错误是由于什么导致的吗，谢谢。同时我也在学你发的网址

sobereva

jia1012428 发表于 2023-2-19 18:33
您好，我用的是acpype网站生成的配体文件。当我用转氨酶与单配体（pmp或mba）的MD时，两个都没有问题。但 ...

我的链接里该说的都说了，没有可补充的

另外，sobtop远比acpype灵活强大，acpype已经完全被我弃了

jia1012428

sobereva 发表于 2023-2-20 02:36
我的链接里该说的都说了，没有可补充的

另外，sobtop远比acpype灵活强大，acpype已经完全被我弃了

收到，谢谢！

jia1012428

sobereva 发表于 2023-2-20 02:36
我的链接里该说的都说了，没有可补充的

另外，sobtop远比acpype灵活强大，acpype已经完全被我弃了

收到，谢谢！