标题: amber求助，在恒压平衡过程中提示密度变化过大停止计算应该如何处理 [打印本页] 作者Author: 肖安炜 时间: 2025-5-17 16:59 标题: amber求助，在恒压平衡过程中提示密度变化过大停止计算应该如何处理 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.
作者Author: KanbeKotori 时间: 2025-5-17 20:25
先用pmemd(.MPI)或sander(.MPI)跑一段时间，让他们重新计算一下nonbond list cells。看密度波动差不多了再换回pmemd.CUDA作者Author: 18217265596 时间: 2025-5-17 21:16
Alternatively you can run with the CPU code until the density has converged
and then switch back to the GPU code.读一遍