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
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>> --
>> 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
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
Received on Wed Apr 13 2011 - 11:00:05 PDT
