That would not be hard to add to PMEMD, but not in a timely manner...
On Wed, Jan 30, 2013 at 9:37 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Sander has some more sophisticated restraints in the nmropt module. I
> think one of the plane-plane angle or plane-point angle can be made to do
> what you want.
>
> Note, though, this is sander only.
>
> HTH,
> Jason
>
> On Wed, Jan 30, 2013 at 11:40 AM, Thomas Evangelidis <tevang3.gmail.com
> >wrote:
>
> > Actually you are right, it is much easier -and technically correct- to
> > enlarge the box rather than doing all these alchemies I described to
> > prevent periodic contacts. I just wanted to avoid equilibrating and
> > recalculating boost parameters for aMD, but it seems inevitable.
> >
> > Just for the record, I would like to know if applying a force along an
> axis
> > without modifying the code is possible?
> >
> > thanks,
> > Thomas
> >
> >
> >
> > On 28 January 2013 12:56, Thomas Evangelidis <tevang3.gmail.com> wrote:
> >
> > > Daniel and Ross,
> > >
> > > I was just asking if there is a way to find atoms from periodic images
> > > within a given cutoff of an atom in the primary cell, something like
> the
> > > "pbwithin" macro of VMD.
> > >
> > > I carefully decided the box dimensions to avoid such effects. The
> protein
> > > C-teminus was pinned down with coordinate restraints to eliminate
> > diffusion
> > > and use a smaller box, as I am only interested in the dynamics o the
> > > N-terminus. It appears that I have set the Z-dimension a few Angstroms
> > > shorter than it should be. In my opinion, that periodic contact
> resulted
> > > from an unnatural stretch on the folded part of the protein and a
> > > concurrent unfolding of the flexible N-terminus that was driven by its
> > high
> > > positive charge and perhaps the ions (I use a NaCl concentration of
> 0.15
> > > mM) that bridge the positive N-term with the negative C-term on the
> > > periodic cell. Since the simulation has progressed too much, I would
> > prefer
> > > to give a flick to the N-term so that it goes away from that position
> and
> > > let the molecule adopt a "more natural" conformation. And of course I
> > will
> > > not include that part of the trajectory in my analysis.
> > >
> > > Is it possible to apply a force along the Z-axis with NMR-based
> > > restraints? I have found an older post in the list which says that
> > > modification to the code must be made.
> > >
> > > thanks,
> > > Thomas
> > >
> > >
> > >
> > >
> > > On 28 January 2013 03:07, Ross Walker <ross.rosswalker.co.uk> wrote:
> > >
> > >> Hi Thomas,
> > >>
> > >>
> > >> This is not possible in AMBER and even if it was I do not believe that
> > it
> > >> will do what you actually think it will do. Any restraint to an image
> > can
> > >> be recast as an internal restraint, since you have periodic boundaries
> > and
> > >> cannot be anything other than this. Placing a minimum distance
> restraint
> > >> between the C terminal of your protein and the N terminal of an image
> is
> > >> exactly the same as placing the same restraint between the two ends of
> > the
> > >> central protein with the distance and sign of the force constant just
> > >> adjusted for the imaging. In effect all you will actually do is squash
> > the
> > >> two ends of your protein together compacting it which is what you
> > >> definitely don't want to do. Ultimately you need to make the size of
> > your
> > >> solute box larger to avoid such periodic artifacts.
> > >>
> > >> All the best
> > >> Ross
> > >>
> > >> On 1/27/13 10:22 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
> > >>
> > >> >Dear AMBER users,
> > >> >
> > >> >I would like to know if distance restraints between the protein in
> the
> > >> >primary cell and one of its periodic images are allowed. The
> C-terminal
> > >> >loop of my protein interacts at some point of the simulation with the
> > >> >N-terminus of the protein in a periodic cell, and stays there for a
> > long
> > >> >time. To avoid that I would like to apply a force that moves away the
> > >> >C-terminal loop whenever it reaching a cutoff distance from the
> > periodic
> > >> >image. Is this possible in AMBER?
> > >> >
> > >> >
> > >> >thanks,
> > >> >Thomas
> > >> >
> > >> >
> > >> >--
> > >> >
> > >>
> >======================================================================
> > >> >
> > >> >Thomas Evangelidis
> > >> >
> > >> >PhD student
> > >> >University of Athens
> > >> >Faculty of Pharmacy
> > >> >Department of Pharmaceutical Chemistry
> > >> >Panepistimioupoli-Zografou
> > >> >157 71 Athens
> > >> >GREECE
> > >> >
> > >> >email: tevang.pharm.uoa.gr
> > >> >
> > >> > tevang3.gmail.com
> > >> >
> > >> >
> > >> >website: https://sites.google.com/site/thomasevangelidishomepage/
> > >> >_______________________________________________
> > >> >AMBER mailing list
> > >> >AMBER.ambermd.org
> > >> >http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >>
> > >> _______________________________________________
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> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > >
> > > ======================================================================
> > >
> > > Thomas Evangelidis
> > >
> > > PhD student
> > > University of Athens
> > > Faculty of Pharmacy
> > > Department of Pharmaceutical Chemistry
> > > Panepistimioupoli-Zografou
> > > 157 71 Athens
> > > GREECE
> > >
> > > email: tevang.pharm.uoa.gr
> > >
> > > tevang3.gmail.com
> > >
> > >
> > > website: https://sites.google.com/site/thomasevangelidishomepage/
> > >
> > >
> > >
> >
> >
> > --
> >
> > ======================================================================
> >
> > Thomas Evangelidis
> >
> > PhD student
> > University of Athens
> > Faculty of Pharmacy
> > Department of Pharmaceutical Chemistry
> > Panepistimioupoli-Zografou
> > 157 71 Athens
> > GREECE
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > _______________________________________________
> > 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
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Received on Sat Feb 09 2013 - 10:30:02 PST
