On Tue, Dec 11, 2012 at 6:01 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> On 12/10/2012 05:29 PM, Jason Swails wrote:
>
>
> > The forces and energies are
> > calculated in different subroutines on a per-restraint basis. If you are
> > looking for a distance, look for the subroutine "disnrg" in nmr.F90.
> This
> > is where the force (and its direction) are calculated. The direction
> comes
> > at the end, where dfr(m) is calculated.
>
> Thanks!
>
> > Also note that, as per Newton's 3rd law, that the force
> > exerted by the restraint on the first atom is the same, but opposite of
> > that on the second atom.
>
> The distance restraint system we're dealing with can be modeled by two
> masses that are connected by a string, while none of the masses is in
> fixed position and the length of the string varies over time, right?
> This system is just superposed on top of the normal force field and
> solved numerically. In this picture it is obvious that the spring
> mediates symmetric forces acting on both atoms. Do we agree :-)?
>
Assuming you meant spring (or a string with spring-like qualities ;)), I
would agree. </joke> This distance restraint acts exactly like a bond does
(except in cases where the distance restraint acts between the COM of
different atom groups -- in this case the forces need to be distributed
over all atoms in the restraint a la chain rule). Nothing in standard MD
is 'anchored' (e.g., like a spring connecting a mass to a wall, where only
the mass oscillates). Of course, you could effectively anchor one atom by
giving it an infinite* mass, in which case no reasonable force will move
it. Even in anchored systems, however, the spring exerts a symmetric
force, only the anchor has an effective infinite mass that prevents any
kind of acceleration.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 11 2012 - 05:30:04 PST
