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搭体系出现了一些问题希望有人能解答
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用Charmm-GUI搭了一个体系，并进行了扩充，在能量最小化时出现了以下问题There is no domain decomposition for 20 ranks that is compatible with the given box and a minimum cell size of 6.2556 nm. Change the number of ranks or mdrun option -rdd. 我在GRomacs的手册上看到了类似的错误--There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm This means you tried to run a parallel calculation, and when mdrun tried to partition your simulation cell into chunks for each processor, it couldn't. The minimum cell size is controlled by the size of the largest charge group or bonded interaction and the largest of rvdw, rlist and rcoulomb, some other effects of bond constraints, and a safety margin. Thus it is not possible to run a small simulation with large numbers of processors. So, if grompp warned you about a large charge group, pay attention and reconsider its size. mdrun prints a breakdown of how it computed this minimum size in the .log file, so you can perhaps find a cause there. If you didn't think you were running a parallel calculation, be aware that from 4.5, GROMACS uses thread-based parallelism by default. To prevent this, you can either give mdrun the "-nt 1" command line option, or build GROMACS so that it will not use threads. Otherwise, you might be using an MPI-enabled GROMACS and not be aware of the fact. 根据他的提示，我在能量最小化的命令行加上了"-nt 1"，结果发现了新的错误Setting the total number of threads is only supported with thread-MPI and GROMACS was comipled without thread-MPI 在没扩充前是可以进行能量最小化的，扩充之后就不可以了，我对Charmm-GUI不太了解，GROMACS也才接触，也不太清楚我的错误rank和手册上的nodes有什么差别，希望懂的人给我一些建议 |
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