On Mon, Jan 29, 2024, Kikuchi, Shinichi via AMBER wrote:
>I am trying to perform a MD simulation of a membrane protein, for which the
>system includes lipids, H2O, and ions, generated by using Packmol-memgen
>found in the amber package. The energy of the total system seems to be
>strange, because the energy calculated by using Gromacs is very different
>from that of amber, for the latter of which is remarkably high in the bond,
>vdW, etc (gromacs is familiar for me).
There should be nothing special here. Please use the "checkstructure"
command in cpptraj, will will identify bad clashes, and might help localize
the problem.
>Although I am a stranger of amber, I think that the pbc settings for lipids
>may be incorrect, bcause some atoms are slightly located in the outside
>from the periodical box.
This feature is almost universal, if I understand you correctly. Atoms that
appear to be outside the box are in the next unit cell over, and there is a
corresponding "hole" or "dent" in the opposite side of the unit cell.
...good luck...dac
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Received on Mon Jan 29 2024 - 08:30:02 PST
