with a single membrane there is no difference between intracellular side
and extracellular side. even if you used some constraint, the line is
arbitrary since the system is periodic. if you want a true division between
the sides, I think you would need a different setup such as a micelle, or 2
parallel membranes.
restraining a ligand to be closer to one side of the membrane than the
other might be reasonable, but that's not the same as what you asked.
On Fri, Jul 9, 2021 at 3:04 PM 王进安 <jawang1985.gmail.com> wrote:
> Hi,
>
> I'm writing this email to check whether AMBER has some functions to
> constrain the ligand in the extracellular side of the membrane. Because in
> the current PBC condition, the ligand could artificially move into the
> intracellular side.
>
> Best regards,
> Jinan
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Fri Jul 09 2021 - 12:30:02 PDT
