请教Amber如何实现在模拟中消除大分子的平动和转动

亚切ss

萌新一枚，之前看过Sob老师的一篇回复，里面提到蛋白和小分子配体这种模拟最好是在模拟中就消除蛋白的平动和转动，后续没能搜到合适的教程，想请教各位大佬在Amber中如何实现这个功能，以保证蛋白可以一直处于水盒的中央

puzhongji

iwrap If iwrap = 1, the coordinates written to the restart and trajectory files will be "wrapped" into a primary
box. This means that for each molecule, its periodic image closest to the middle of the "primary box"
(with x coordinates between 0 and a, y coordinates between 0 and b, and z coordinates between 0
and c) will be the one written to the output file. This often makes the resulting structures look better
visually, but has no effect on the energy or forces. Performing such wrapping, however, can mess
up diffusion and other calculations. If iwrap = 0, no wrapping will be performed, in which case it is
typical to use cpptraj as a post-processing program to translate molecules back to the primary box.
For very long runs, setting iwrap = 1 may be required to keep the coordinate output from overflowing
the trajectory and restart file formats, especially if trajectories are written in ASCII format instead of
NetCDF (see also the ioutfm option). Default = 0.

亚切ss

puzhongji 发表于 2023-2-19 09:23
iwrap If iwrap = 1, the coordinates written to the restart and trajectory files will be "wrapped" in ...

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