求助加速动力学时报错： Calculation halted

吹呀4344 · 发表于 Post on 2023-9-7 16:57:13

我在执行加速动力学的时候报错，查询网上是体系还没有收敛的原因。我做的是蛋白小分子体系，但是小分子是带磷酸基团的，
所以我缩小了平衡时的步数，但是没有缩短总时长。常规md能跑，但是加速动力学时就崩溃了。
想询问大佬，我该怎么调整我的in文件，已经每一步平衡，我该观察什么指标来了解体系是否收敛了呢？

01_min.in (238 Bytes, 下载次数 Times of downloads: 11)

02_heat.in (399 Bytes, 下载次数 Times of downloads: 8)

03_density.in (388 Bytes, 下载次数 Times of downloads: 14)

04_equil.in (360 Bytes, 下载次数 Times of downloads: 9)

05_prod.in (374 Bytes, 下载次数 Times of downloads: 10)

06_gamd_0.in (506 Bytes, 下载次数 Times of downloads: 15)

ERROR: Calculation halted.  Periodic box dimensions have changed too much from their initial values.
  Your system density has likely changed by a large amount, probably from
  starting the simulation from a structure a long way from equilibrium.

  [Although this error can also occur if the simulation has blown up for some reason]

  The GPU code does not automatically reorganize grid cells and thus you
  will need to restart the calculation from the previous restart file.
  This will generate new grid cells and allow the calculation to continue.
  It may be necessary to repeat this restarting multiple times if your system
  is a long way from an equilibrated density.

  Alternatively you can run with the CPU code until the density has converged
  and then switch back to the GPU code.

of length = 42Failed an illegal memory access was encountered

LUOD · 发表于 Post on 2023-10-13 20:33:59

请问现在知道了吗，我也经常遇到这个问题

c00jsw00 · 发表于 Post on 2023-11-3 14:22:12

1.資料: https://sourceforge.net/p/gamd/mailman/gamd-discuss/?page=4
2.
We have also found bugs with LiGaMD in AMBER22, due to some mismatched code updates in related GPU TI functions.
While we are trying to resolve the issues, could you perhaps try LiGaMD in AMBER 20 if you have access to the package?
Best,
Yinglong
3.使用amber20吧我是這樣解決的這一個bug 應該還沒fix

PotterDai · 发表于 Post on 2023-11-3 14:31:49

个人建议改用较小的electrostatic cutoff 或者增大盒子边界与 soulte 的距离。原因在报错里也说了，主要是与周期性边界有关。另外一个可以尝试的是用八面体盒子代替立方体盒子，建议 lz 试试

Huschein · 发表于 Post on 2023-11-27 18:07:06

本帖最后由 Huschein 于 2023-11-27 21:46 编辑

同样，我今天做LiGaMD也遇到这个问题，amber22
如果你是递交到集群的话，我建议你可以尝试我的办法，因为我之前用gmx递交到集群的时候也会出现类似问题，可能就是GPU/域分解和压力耦合的问题，具体什么原因造成的我不清楚，我不了解底层，但是无论是gmx还是amber，基本上你只要把taup改大一些就可以（建议从10到25到50这样去试试），这基本上可以解决这个问题，但是至于MD模拟的合理性，我这里不谈，大家自己看就好了

如果还不行建议在你的in文件中加入
&ewald
skinnb=5,
/
目的就是计算截断更长，可能精度更高就不会这样了
参考：http://archive.ambermd.org/202006/0200.html

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[Amber] 求助加速动力学时报错： Calculation halted

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