no, because here the user needs to restrain the COM of some atoms to a
specific location in space (center of the box). I don't think that's
supported.
On Wed, Apr 13, 2011 at 2:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Apr 13, 2011 at 10:53 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> you would need to be able to define several independent flatwell COM
>> restraints (1 for each chain) - can the current code do that?
>>
>
> I think so... Isn't that what we do when we create chirality restraints for
> REMD simulations (or something of the sort)? Of course I may be getting
> some related functionalities confused here
>
>
>> 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
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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 - 12:00:02 PDT
