Hi Ken!
The best advice I can give here is that Amber isn't a program that does
hard-sphere potentials, so if you want particles to suddenly hit an
infinite wall when they travel within (or outside of) some distance of one
another you'll need a separate code. The closest you could get would be to
use the nmropt (NMR optimization) features to implement HARMONIC restraints
on either side of a flat-bottom potential. Particles connected by such a
potential experience no forces (at least, no forces due to one another) so
long as they are within some small distance of on another, but begin to
experience harmonic attraction as the distance crosses that threshold.
Depending on what exactly you want to simulate, I can recommend different
programs. How many particles (atoms) will your system have? Do you want
periodic boundary conditions, to simulate the effect of having a fairly
elaborate density of material, or are you content to see just a few of
these molecules interact in the gas phase, off in an otherwise empty region
of space?
Dave
On Mon, Apr 4, 2016 at 2:03 PM, Kenneth McGuinness <
kenneth.mcguinness.gmail.com> wrote:
> Hi everyone,
>
> This is my first post to this forum and I am grateful to be a part of it!
>
> I am relatively new to Amber as well. Sorry if this post goes over material
> that someone else has posted before. I have looked as far as I could and I
> did not find an exact match on what I am looking to do.
>
> So without going into the entire project,
>
> I would like to run simulations in vacuo using spherical flatwell
> potentials.
>
> I am not sure how to implement this - however this article has implemented
> the method (this paper is similar to my work - and the method will greatly
> help my work)
>
> http://pubs.acs.org/doi/abs/10.1021/jp501503x
>
> Any help in setting this up would be very much appreciated - I am still
> trying to decipher what section 24.1 means in the Amber doc. Please let me
> know any details that are needed from me in order to progress.
>
> I greatly appreciate any and all help!
>
> Thank you!
>
> With gratitude,
>
> ~Kenneth
>
> Kenneth N. McGuinness Ph.D
> Research Associate
> Advanced Science Research Center CUNY
> Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
> Cell: 928-925-7693
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>
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Received on Mon Apr 04 2016 - 12:00:03 PDT
