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[Amber] 求助 平衡系统时,盒子逐渐变大,溶剂和蛋白分开

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本帖最后由 watermelon_ 于 2024-11-7 13:57 编辑

最小化和加热系统后,进行npt时,盒子开始逐渐变大,出现大量空隙,溶剂和蛋白分割成体积和间隔相似大小的团块
报错内容是

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.

使用的in文件均来自官网教程https://ambermd.org/tutorials/basic/tutorial13/index.php
而且我用官网教程里面提供的top结构做,也会出现这样的问题

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