求助gromacs在有机溶剂体系的平衡相模拟计算过程中出现吐核错误

Snown · 发表于 Post on 2022-3-29 23:51:56

各位老师好，我在不同有机溶剂体系中模拟沥青质的聚集行为，但在平衡相模拟过程中断，终端中出现“段错误（吐核）”的字样，具体警告内容如下所示。想请教一下为什么会出现“吐核”错误，该错误出现后应该从哪个文件入手进行修改呢？谢谢。
WARNING: Using the slow plain C kernels. This should not happen during routine usage on supported platforms.starting mdrun 'asp-box2'
500000 steps, 1000.0 ps.
step 2700, will finish Wed Mar 30 12:13:53 2022
Step 2761, time 5.522 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000011, max 0.000107 (between atoms 2537 and 2573)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2189 2237 30.4 0.1090 0.1090    0.1090
2190 2238 31.0 0.1090 0.1090    0.1090

Step 2769, time 5.538 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.270460, max 37.492767 (between atoms 2190 and 2238)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2189 2237 90.0 0.1090 3.6836    0.1090
2190 2238 90.0 0.1090 4.1957    0.1090
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 2184 and 2238
at distance 4.286 which is larger than the table limit 2.009 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason.

Step 2770, time 5.54 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000658, max 0.119843 (between atoms 2189 and 2237)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2189 2237 90.0 3.6836 0.1221    0.1090
2190 2238 90.0 4.1957 0.1110    0.1090

Step 2771, time 5.542 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.244306, max 33.750931 (between atoms 2190 and 2238)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2189 2237 90.0 0.1221 3.3524    0.1090
2190 2238 90.0 0.1110 3.7879    0.1090
Wrote pdb files with previous and current coordinates

Step 2772, time 5.544 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000011, max 0.000082 (between atoms 4518 and 4571)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2185 2235 62.9 0.1094 0.1090    0.1090
2188 2236 58.0 0.1094 0.1090    0.1090
2190 2238 32.7 3.8030 0.1090    0.1090

Step 2773, time 5.546 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.103036, max 18.976585 (between atoms 2190 and 2238)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2185 2235 55.2 0.1090 0.1090    0.1090
2188 2236 49.7 0.1090 0.1090    0.1090
2189 2237 70.7 0.1090 0.1090    0.1090
2190 2238 90.0 0.1090 2.1774    0.1090
Wrote pdb files with previous and current coordinates

Step 2774, time 5.548 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 13846.613281, max 2526945.750000 (between atoms 2192 and 2239)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
2185 2235 90.0 0.1090 0.6697    0.1090
2189 2237 90.1 0.1090 17540.2715    0.1090
2190 2238 89.7 2.1774 15725.8203    0.1090
2192 2239 90.0 0.1080 272910.2500    0.1080
2208 2244 90.0 0.1080 28832.7930    0.1080
Wrote pdb files with previous and current coordinates
段错误(吐核)