One thing I forgot to mention is that I'd probably set nscm=0 so it never
removes COM motions.
On Wed, Apr 13, 2011 at 12:19 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> 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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>> >> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >> >>>
>> >> >>
>> >> >> _______________________________________________
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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
>> > _______________________________________________
>> > 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
>
--
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 - 12:30:04 PDT
