I am pretty aware of this. The piece of solid surface
is here in this context the same isolated molecule
like any other (protein for example). In case of solid surface we can speak
about "raft" floating in the water box.
So for this kind of simulation it is important:
#1
To place given ligand (like in my case PU ) in the central part of
sufficiently
big surface area to decrease enough effect of surface border ( which is
source of field inhomogeneities ).
#2
To have sufficient distance between surf. images in the direction
perpendicular to the surface to
decrease sufficiently electrostatic interaction of the given ligand with
surf. periodic images.
Best,
Marek
Dne Wed, 04 Aug 2010 13:23:11 +0200 case <case.biomaps.rutgers.edu>
napsal/-a:
> On Wed, Aug 04, 2010, Tom Williams wrote:
>>
>> I am wondering if Amber can simulate the infinite *mobile* surface.
>> The surface is NOT fixed with position or frozen, but is actually
>> bonded with PBC images
>> though PBC box boundaries.
>> PBC
>> image | simulat. cell | PBC image
>> For example: for the suface -A-B-C-: in PBC
>> ----A----B----C-----A----B----C------A----B----C
>>
>> Does Amber have this kind of functionalities?
>
> No....only nonbonded forces can operate across unit cell boundaries.
>
> ...dac
>
>
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Received on Wed Aug 04 2010 - 08:30:12 PDT
