我在做gromacs的模拟，在里面加入沥青质，C6,C7,C8H10,C25等分子。在跑模拟时一直崩溃，找不到解决方法。
输命令时没有warning提示，只有一个note
NOTE 1 [file eq.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.
下面是warning
GROMACS: gmx mdrun, version 2020.6-MODIFIED
Executable: C:\gmx2020.6_AVX2_CUDA_win64\gmx2020.6_GPU\bin\gmx.exe
Data prefix: C:\gmx2020.6_AVX2_CUDA_win64\gmx2020.6_GPU
Working dir: G:\chw\A1-C25
Command line:
gmx mdrun -v -deffnm eq
Reading file eq.tpr, VERSION 2020.6-MODIFIED (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads
Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
starting mdrun 'mixbox'
50000000 steps, 50000.0 ps.
step 13300: timed with pme grid 84 84 84, coulomb cutoff 1.000: 148.0 M-cycles
step 13500: timed with pme grid 72 72 72, coulomb cutoff 1.157: 142.2 M-cycles
step 13700: timed with pme grid 64 64 64, coulomb cutoff 1.302: 188.1 M-cycles
step 13900: timed with pme grid 72 72 72, coulomb cutoff 1.157: 177.1 M-cycles
step 14100: timed with pme grid 80 80 80, coulomb cutoff 1.042: 165.1 M-cycles
step 14300: timed with pme grid 84 84 84, coulomb cutoff 1.000: 173.7 M-cycles
optimal pme grid 72 72 72, coulomb cutoff 1.157
step 6373800, will finish Thu Dec 5 15:53:59 2024
Step 6373899, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000012 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 44.9 0.0973 0.0973 0.0973
Step 6373900, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000018 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 39.6 0.0973 0.0973 0.0973
step 6373900, will finish Thu Dec 5 15:53:58 2024
Step 6373901, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000030 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 37.1 0.0973 0.0973 0.0973
Step 6373902, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000042 (between atoms 756 and 784)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 35.9 0.0973 0.0973 0.0973
Step 6373903, time 6373.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000049 (between atoms 756 and 783)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 37.3 0.0973 0.0973 0.0973
Step 6374897, time 6374.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000033 (between atoms 729 and 767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 55.8 0.0973 0.0973 0.0973
Step 6374898, time 6374.9 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000002, max 0.000045 (between atoms 729 and 767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
759 785 55.1 0.0973 0.0973 0.0973
Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem