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标题: nvt步骤报错了（LINCS WARNING） [打印本页]

作者
Author: jia1012428 时间: 2023-2-18 09:00
标题: nvt步骤报错了（LINCS WARNING）
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

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

作者
Author: jia1012428 时间: 2023-2-18 17:19

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！

作者
Author: jia1012428 时间: 2023-2-19 18:33

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

作者
Author: sobereva 时间: 2023-2-20 02:36

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

作者
Author: jia1012428 时间: 2023-2-20 22:13

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！

作者
Author: jia1012428 时间: 2023-2-20 22:14

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！

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