the OP said something about studying aggregation.
On Wed, Apr 13, 2011 at 1:55 PM, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> for different chains probably not, but I did not get the idea that there
> were more than one chain. Anyways, Carlos is right, should not be more
> than a small number of lines of code.
>
> Adrian
>
>
> On 4/13/11 7:53 PM, Carlos Simmerling wrote:
>> 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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>>>>
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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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>>
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 13 2011 - 11:30:03 PDT
