求助gromacs计算显示“内部错误，总势能非常高”

saga · 发表于 Post on 2024-11-6 15:04:24

采用gromacs计算电解液分子动力学，输出文件错误显示为“Internal error(bug):

Step 0: Thetotal potential energy is 3.72084e+18, which is extremely high.

The LJ andelectrostatic contributions to the energy are 3.72084e+18 and

5012.68,respectively. A very high potential energy can be caused by

overlappinginteractions in bonded interactions or very large coordinate

values. Usuallythis is caused by a badly- or non-equilibrated initial

configuration,incorrect interactions or parameters in the topology.”

下面是上传的相关文件。请大神指点!

atomstyle.itp (878 Bytes, 下载次数 Times of downloads: 0)

BOB.itp (9.83 KB, 下载次数 Times of downloads: 0)

em.mdp (379 Bytes, 下载次数 Times of downloads: 0)

eq.mdp (776 Bytes, 下载次数 Times of downloads: 0)

FEC.itp (7.82 KB, 下载次数 Times of downloads: 0)

Li.itp (197 Bytes, 下载次数 Times of downloads: 0)

PC.itp (10.62 KB, 下载次数 Times of downloads: 0)

run.top (464 Bytes, 下载次数 Times of downloads: 0)

slurm-3949027.out (77.52 KB, 下载次数 Times of downloads: 0)

sobereva · 发表于 Post on 2024-11-6 15:31:55

不要自己在标题里手写【求助】这种标签，http://bbs.keinsci.com/thread-9348-1-1.html里明确说了。这次给你改了，以后注意

saga · 发表于 Post on 2024-11-6 15:33:58

收到，谢谢sobereva老师提醒，下次一定注意!

sobereva · 发表于 Post on 2024-11-9 08:30:36

参考http://sobereva.com/soft/Sobtop#FAQ8进行排查。虽然里面说的是MD的情况，但其中很多不合理的因素在em阶段就已经会造成严重问题

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[GROMACS] 求助gromacs计算显示“内部错误，总势能非常高”