24小时热门版块排行榜

>论坛更新日志 (4819)
>导师招生 (397)
>虫友互识 (289)
>休闲灌水 (247)
>文献求助 (202)
>招聘信息布告栏 (161)
>硕博家园 (138)
>论文道贺祈福 (127)
>考博 (85)
>考研 (80)
>找工作 (64)
>基金申请 (63)
>博后之家 (61)
>论文投稿 (39)
>教师之家 (38)
>公派出国 (35)

返回列表

当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖

戍角悲丶丶

金虫 (小有名气)

应助: 2 (幼儿园)
金币: 506.3
红花: 2
帖子: 245
在线: 74.6小时
虫号: 2783626
注册: 2013-11-06
性别: GG
专业: 理论和计算化学

[求助] 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已有1人参与

各位大神，求解决，重谢！！！
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

回复此楼