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
> >>>
> >>>
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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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 13 2011 - 11:30:04 PDT
