On Wed, Apr 13, 2011 at 11:38 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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.
>
Oh I see what you mean. I still think it can be done with the existing
code, you just have to play tricks :). This is how I would do it: create a
dummy atom in leap with no charge, no mass, and only a tiny, tiny van der
waals radius to prevent any catastrophic collapse, and put it at 0,0,0.
Then you *always* run with ntr=1, and the restraint mask is just that dummy
atom, so that you can make sure it doesn't move (much). If you define all
of the distances in the nmr restraint file with respect to that dummy atom,
you can effectively hold all of the chains within a common sphere.
As long as you can stand using a sphere instead of a cube/box, I think
that's all you need to do. Another option, of course, is the solvent cap
that Dave mentioned, but I'm not sure how that works exactly.
All the best,
Jason
> 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
> >> >>>
> >> >>>
> >> >>> _______________________________________________
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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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> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
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> > 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
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Received on Wed Apr 13 2011 - 12:30:03 PDT
