Re: [AMBER] Implicit solvent and box

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 13 Apr 2011 14:01:16 -0400

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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 13 2011 - 11:30:03 PDT
Custom Search