Hi Carlos,
Two parallel membranes sounds like a good idea although it will increase
the system size.
Thanks,
Jinan
On Fri, Jul 9, 2021 at 2:08 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
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> > 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
