Adding to carlos' comments
I think one can use the code 'as is' and get the results anyways.
You can use a flat-well potential restraint on the center of mass of the
system. That, plus a large force constant for the parabolic part of the
restraint should keep the center of mass of the protein within a box.
Adrian
On 4/13/11 7:46 PM, Carlos Simmerling wrote:
> 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
>>
>>
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Apr 13 2011 - 11:00:03 PDT
