Hey Dave - great to hear from you!
I wrote my comments in-line to help with following the conversation
On Mon, Apr 4, 2016 at 2:32 PM, David Cerutti <dscerutti.gmail.com> wrote:
> 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 type of potential I am looking to implement is the one implemented in
section 4.3.2 with option (g=2 sphere) in this link:
ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf
I tried gromacs but it does not implement GPU usage yet with vacuum/and no
pbc -speed is the biggest need right now- Amber does conveniently
> 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.
Not sure how to do this in a 3D sense (spherical) in terms of the DISANG
options and restraint files (gromacs has a simple format) I have not
wrapped my head around Amber's way of doing it yet :-)
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?
~1000-10,000 atoms
> 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?
>
I am setting up a screening process for molecular interactions
1. Speed is the most important part so I intend on using the gas phase
without periodic boundaries
2. Once I see interactions worth pursuing in (1) I will then add more
molecular details (implicit, explicit solvent, pbc etc.) in the force field
to rule out interactions worth testing in the lab.
3. The spherical potentials prevent the molecules from drifting too far
into space because of the lack of viscosity
I am really grateful for your time!
Any more details I can give? Please lmk
Thank you Dave!
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Apr 04 2016 - 12:00:05 PDT
