On Tue, Feb 08, 2022, Tucker Burgin wrote:
>I am interested in a simulation involving a large protein homodimer. In
>order to save computational resources it would be ideal if I could simulate
>only a single full protein that interacts with its own image across a
>periodic boundary; however, for this to work, I would need a way to
>"invert" the boundary condition to obtain the desired symmetry. I'm after
>something like this (hope the ASCII schematic comes through clearly):
>
>__A__________
>| | |
>| d|p |
>| d|p |
>| d|p |
>| | |
>----------------A'----
>
>Where A on the left is the simulation box containing the protein d,
>interacting with the mirror image A' on the right containing a mirror image
>of the protein, p.
>
>Is anyone aware of a way to implement this sort of boundary condition in
>Amber? Is this more trouble than it's worth?
I don't think Amber has any such capabilities. The "more trouble than it's
worth" idea sounds correct to me. I'm pretty sure CHARMM can enforce
symmetries, and maybe other programs can as well. But even that would be an
artificial restraint -- what if a water molecule wanted to enter the
interface region?
...good luck....dac
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Received on Wed Feb 09 2022 - 06:00:02 PST
