求助：Gromacs运行ED任务时出错

1121571266

最近在学习Gromacs的主成分动力学，首先正常跑了下MD任务（体系很小，只有两个苯分子），用轨迹做了协方差分析得到了本征值和本证向量，然后使用以下命令生成了edi文件：
gmx_mpi_d make_edi -f eigenvec.trr -eig eigenval.xvg  -s run.tpr -o run.edi -linacc 1 -accdir "+1 +1 +1" -ori Model.gro
后将这个edi文件和生成edi文件时使用的tpr文件传递给mdrun运行ED任务，结果出现以下报错：

             :-) GROMACS - gmx mdrun, 2022.2 (double precision) (-:

Executable:   /public1/home/sch0015/Gromacs/DOUBLE-mpi/install/bin/gmx_mpi_d
Data prefix:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/install
Working dir:  /public1/home/sch0015/Gromacs/DOUBLE-mpi/jobs/edy
Command line:
  gmx_mpi_d mdrun -s run.tpr -ei run.edi -eo ed.xvg

Compiled SIMD: AVX2_256, but for this host/run AVX_512 might be better (see
log).
Reading file run.tpr, VERSION 2022.2 (double precision)
Changing nstlist from 10 to 100, rlist from 1.2 to 1.2

NOTE: Periodic molecules are present in this system. Because of this, the domain decomposition algorithm cannot easily determine the minimum cell size that it requires for treating bonded interactions. Instead, domain decomposition will assume that half the non-bonded cut-off will be a suitable lower bound.
Using 8 MPI processes

Non-default thread affinity set, disabling internal thread affinity

Using 1 OpenMP thread per MPI process

ED: Initializing essential dynamics constraints.
ED: Reading edi file run.edi
ED: Note: Reference and average structure are composed of the same atom indices.
ED: Found 1 ED group.
ED: Initial RMSD from reference after fit = 0.000000 nm
ED: Fitting origin structure to reference structure
starting mdrun 'Model'
100000 steps,    100.0 ps.

-------------------------------------------------------
Program:     gmx mdrun, version 2022.2
Source file: src/gromacs/linearalgebra/nrjac.cpp (line 164)
MPI rank:    1 (out of 8)

Fatal error:
Error: Too many iterations in routine JACOBI

希望论坛里有懂ED的大神帮助下，很久了一直都是这个报错，网上找了资料好像这个报错和“结构对齐”有关，但是至今没有头绪，期待大家的帮助，万分感谢！

1121571266

没有人懂吗？？？？

k64_cc

我本来想说PCA CV用Plumed可能会好一些，但是从零开始学plumed可能会更加的抽象…应该很难帮上你。

jiahui

1121571266 发表于 2023-8-14 13:09
没有人懂吗？？？？

我也碰到了这个问题，你解决了吗？
求指点