if you want a "box" that's not quite the same as periodic. it's fairly
easy in Amber to add a restraint to keep things inside a cube- I did
this a while back using a flatwell restraint for the 3 Cartesian
coordinates on each atom. So I think you need to decide if you just
want to confine things, or if you need real periodicity. Confinement
is not hard to add, but of course that assumes you know how to write a
dozen or so lines of code.
On Wed, Apr 13, 2011 at 12:47 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Apr 13, 2011, Elisa Frezza wrote:
>>
>> I would like to ask you if I can perform MD simulation using implicit
>> solvation model and a cubic box to confine my systems.
>
> No: the implicit solvent models in Amber don't know about periodic
> boundary conditions.
>
> It might be possible to include a "solvent cap" (without solvent!) to confine
> the systems, but the physics of this is very different than periodic boundary
> conditions.
>
> ...regards...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 13 2011 - 11:00:02 PDT
