Dear AMBER Mailing List,
What's the best way to check the minimum/closest distance between periodic
images of the protein molecule being simulated (in periodic box) by AMBER?
In addition, after converting AMBER files to GROMACS ones by
amb2gro_top_gro.py, I'm curious to know how the period box is handled.
Besides a cubic box, AMBER has a truncated octahedron whereas GROMACS has a
dodecahedron. Can GROMACS correctly handle a truncated octahedron and vice
versa?
Thanks,
Yun
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 10 2023 - 15:30:02 PDT
