求助gromacs 混合体系npt时出现问题

yinzi

前期用packmol建立了6nm的盒子，在其中放置了一个多肽。在把packmol生成的pdb文件放入gromacs时，由于出现overlap，em无法进行，重新 editconf生成-box 8 8 8的盒子后，em和nvt都很稳定，但是npt时出现一下问题。我想问是什么原因？
tolerance 2.0
filetype pdb
output mixed.pdb

structure edit.pdb
  number 1
  inside box 0. 0. 0. 60. 60. 60.
end structure

structure jz1.pdb
  number 1455
  inside box 0. 0. 0. 60. 60. 60.
end structure

structure water.pdb
  number 446
  inside box 0. 0. 0. 60. 60. 60.
end structure

Fatal error:
step 128075: The domain decomposition grid has shifted too much in the
Z-direction around cell 3 0 2. This should not have happened. Running with
fewer ranks might avoid this issue.

yinzi

在进行npt时会出现以下error，后续尝试了-rdd 1.4.但是依旧会出现，请问这是什么原因？


Fatal error:
step 103150: The domain decomposition grid has shifted too much in the
Z-direction around cell 3 0 2. This should not have happened. Running with
fewer ranks might avoid this issue.

sobereva

不用mpi并行，只用openmp并行再试。（mdrun加上-ntmpi 1）
等跑一阵子体系稳定了之后再改成默认情况（允许mpi并行因而允许域分解）