|
|
现在问题是不修复蛋白，蛋白的拓扑文件构建失败，但是如果修复蛋白的话在能量最小化的时候会失败
这是失败的指令：D:\autodock\benfagromacs>gmx mdrun -v -deffnm em
:-) GROMACS - gmx mdrun, 2025.2 (-:
Executable: D:\fenzidonglixuemoniruanjian\GROMACS-2025.2_GPU_Windows-AMD64-AVX2_CUDA1263_msvc\bin\gmx.exe
Data prefix: D:\fenzidonglixuemoniruanjian\GROMACS-2025.2_GPU_Windows-AMD64-AVX2_CUDA1263_msvc
Working dir: D:\autodock\benfagromacs
Command line:
gmx mdrun -v -deffnm em
Reading file em.tpr, VERSION 2025.2 (single precision)
1 GPU selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 1 MPI thread
Using 16 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 3.39863e+16 Fmax= inf, atom= 182
Step= 14, Dmax= 1.2e-06 nm, Epot= 3.39863e+16 Fmax= inf, atom= 182
Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 3.3986272e+16
Maximum force = inf on atom 182
Norm of force = inf
GROMACS reminds you: "A little less conversation, a little more action, please." (Elvis Presley) |
|
发表于 Post on 2026-1-5 18:39:43
|
只看该作者 Only view this author
|只看大图 View big picture
|倒序浏览 Reverse view
|阅读模式 Reading model
收藏 Add to favorites
楼主 Author
发表于 Post on 2026-1-6 01:21:59