Hi Jason,
On Wed, Oct 26, 2011 at 11:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Oct 26, 2011 at 6:25 PM, Mo Chen <mc842.cornell.edu> wrote:
>
> > Dear Amber users/developers,
> > May I ask if the direction of the random forces in SMD simulation could
> be
> > defined somehow?
>
>
> What random forces are you talking about? The only random forces I know
> about implemented in Amber right now are in Langevin dynamics, and that has
> nothing to do with SMD. The force induced by the moving umbrella potential
> is in no way random. It is deterministic, and analytically calculated from
> functional form of the potential (it's just a quadratic equation).
>
>
> Sorry I was not phrasing it correctly, and actually I meant to say that the
direction of the force vector is not determined at each SMD pulling step so
that the speed is intended to be a constant, as far as I understand.
> > And are all the variables listed in the example input
> > files? Or can I use all the variables introduced in NMR &rst list? Thank
> > you
> > very much!
> >
>
> I don't know what example input files you're looking at, but you should
> restrict yourself to defining an umbrella potential. That is, set r1 very
> low, to the point that the system will never sample that value or past it,
> set r2=r3 so there's no "flat well" potential, set r4 to be very large to
> the point that the system will never sample that value or past it, and set
> rk2=rk3 so the potential is symmetric. Then you can define the starting
> position of the potential and the ending position of the potential (I can't
> remember how off the top of my head, it's in the manual), and use nstlim to
> control how quickly the coordinate is changed.
>
> That's about the extent of the flexibility you have with SMD (but do you
> need any more?). The main issue is calculating free energies (which is an
> equilibrium quantity) through these non-equilibrium processes. You'll need
> the Jarzynski equation for this, and you need to satisfy the conditions of
> this equation for a valid process.
>
I understand the theory of this. And I am trying to pull the ligand of a
protein from one position to another by pulling one atom of the ligand from
the initial position to the final position. So in this case I wish I could
define the direction of the force beyond the atom to atom distance
constraint. And I wonder if it is possible? Thank you very much!
>
> HTH,
> Jason
>
> HTH,
> Jason
>
>
> >
> > Best,
> > Mo Chen
> > Graduate student
> > Cornell University
> > Ithaca, NY 14850
> > _______________________________________________
> > 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
> _______________________________________________
> 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
Received on Wed Oct 26 2011 - 22:30:02 PDT
