yeap, but I guess what he meant with "asymetric" box is: well, if I'm
pulling on z direction, I can choose to have 10A from each border and say,
20A from the upper z border, then I'm free to stretch the biological stuff
and still be within the 10A safe distance and moreover be inside the
original image, and avoid later work on re-imaging everything to the
original box.
On NAMD it's pretty easy, because you really design the box, based on the
basic vectors, like the solid state vectors of the lattice. But how to
construct such an "elongated z-direction" box on AMBER?
Because if I set the distance bigger than 10A, I will do that on the 3
spatial coordinates, and spend water in xy plane which is not needed....
On Tue, Jul 26, 2011 at 4:21 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> that is correct, but one has to be careful.
>
> Basically, you need to have enough buffer in your box to not be close to
> your image EVER. In the case we are discussing, the final snapshot,
> where one is fully extended, i sthe one one needs to design the box around.
>
> My comment earlier had to do with the fact that you do not need to put
> the initial complex at the edge of the box. You can put it in the middle
> and the system will adjust later on. There might be slight issue if one
> of the proteins gets out of the initial box, but that would be a 'bug'
> due to a bad calculation of distances.
>
> Adrian
>
>
> On 7/26/11 9:15 PM, Bruno Rodrigues wrote:
> > Dear Dr. Adrian,
> >
> > Now I have a question concerned your answer to the last topic on this
> email.
> >
> > Considering a periodic box, and a protein inside with, say, 10 angstrons
> > from the last atom to the border of the box. If your pulling exceeds 10A,
> > then you will end up out of the box. Therefor, you will get inside the
> box
> > from the other side, but you will be very close to your nearest image,
> won't
> > you?
> >
> > I'm asking it because I work with DNA, and we always extend the box a
> little
> > bit on the direction of pulling to avoid these effects. What do you
> think?
> >
> > Thanks
> >
> > On Tue, Jul 26, 2011 at 7:01 AM, Adrian Roitberg<roitberg.qtp.ufl.edu
> >wrote:
> >
> >>
> >>
> >> On 7/26/11 11:32 AM, Sergey Samsonov wrote:
> >>> Dear all,
> >>>
> >>> I've been starting testing steered MD for some systems in order to
> apply
> >>> it for protein-protein interactions analysis and I've been searching
> the
> >>> literature on this topic. I have some related questions, which maybe
> you
> >>> could help me to answer.
> >>
> >> some VERY biased answers below !
> >>
> >>>
> >>> 1. Force of pulling proteins or receptor/ligand apart. In AMBER 10
> >>> manual example the constant of 5000 kcal/(mol A^2) is used. In the
> >>> literature I've seen absolutely different ranges of these values (down
> >>> to 1kcal/(mol A^2)). The explanations are a bit controversial: in some
> >>> papers the authors claim that the constant should be comparable to
> kT/2,
> >>> in other that this constant should be essentially higher in order to
> >>> have less effects from thermal motions. What do you think is
> appropriate
> >>> and what is the best way to optimize this constant for each individual
> >>> system? For pulling ion apart from the protein I noticed quite a
> >>> significant influence of this constant on the calculated free energy.
> >>
> >> First, kT/2 has units of kcal/mol while the force constant has units of
> >> 1kcal/(mol A^2) (for a distance), so the text 'The explanations are a
> >> bit controversial: in some papers the authors claim that the constant
> >> should be comparable to kT/2,in other that this constant should be
> >> essentially higher in order to have less effects from thermal motions.'
> >> makes no sense. Can you make it clearer what you mean ?
> >>
> >> The value of the force constant AND the speed of pulling depend
> >> crucially in what you want to do. Are you using this data to get some
> >> general idea of the protein-protein association pathway or you really
> >> want the free energy? If you want the free energy, then you need to
> >> repeat the pulling MANY times, from an initially 'equilibrated' sampled,
> >> where all the snapshots have the same distance. Then, look at Schulten
> >> papers where he describes the so-called stiff spring approximation. The
> >> force constant CANNOT be very small, otherwise what the pulling spring
> >> and your molecules are doing is very different. Basically, you pull with
> >> a soft spring, and the molecule just does not care and does not follow
> >> the distance.
> >>
> >>
> >>>
> >>> 2. Speed of pulling. Again, I found various values in the literature
> >>> with the range from 1 to 100 A/ns. Am I right if I consider an ability
> >>> of the simulation to keep the structures of pulled apart proteins
> >>> undistorted as one of the most important criteria for the selection of
> >>> this parameter?
> >>
> >> The speed of pulling is extremely system dependent. For free energies,
> >> there are too many tricks to do to explain in this space. Take a look at
> >> the paper below for some ideas.
> >>
> >> Xiong, Hui; Crespo, Alejandro; Marti, Marcelo; Estrin, Dario; Roitberg,
> >> Adrian E.. Theoretical Chemistry Accounts. 116(1-3):338-346 (2006)
> >>
> >>
> >>>
> >>> 3. Is there an explicit way in AMBER (I use AMBER 10) to apply the
> >>> pulling forces to the centers of masses of protein/protein pair or to
> >>> all backbone atoms instead of choosing only two atoms? Otherwise could
> >>> an alternative solution be just putting restraints on backbone or
> >>> C-alpha atoms of the proteins and applying the pulling force on two
> >>> atoms (though this sounds to me being physically more ambiguous)?
> >>
> >> Yes, look at group restraints. You can set a distance between center of
> >> masses of group for instance. Look at the manual also for natural
> >> language restraints.
> >>
> >>>
> >>> 4. Is there the way in Leap to create an assymetric water box for PBC
> >>> with an elongated side, along which the pulling is occuring? This would
> >>> save the computational expenses a lot in case of SMD.
> >>
> >> I am pretty sure this is not needed ! Since you are using PBC, the box
> >> is never really assymetric anyways. If you have your molecule to one
> >> side of the box, then the molecular in the next box is also displaced,
> >> so you gain nothing.
> >>
> >> Adrian
> >>
> >>>
> >>> Thank you very much in advance!
> >>>
> >>> Best regards,
> >>>
> >>> Sergey
> >>>
> >>
> >> --
> >> Dr. Adrian E. Roitberg
> >> Full Professor
> >> Quantum Theory Project, Department of Chemistry
> >> University of Florida
> >>
> >> on Sabbatical in Barcelona until August 2011.
> >> Email roitberg.ufl.edu
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> Full Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Tue Jul 26 2011 - 13:00:02 PDT
