you would need to be able to define several independent flatwell COM
restraints (1 for each chain) - can the current code do that?
On Wed, Apr 13, 2011 at 1:49 PM, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> 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 - 11:00:04 PDT
