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
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> 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 Wed Jan 30 2013 - 10:00:02 PST
