From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Sep 23 2003 - 10:52:14 CDT
If your sphere is hard but the other atoms are not, then you really have a
soft potential using the VDW radii of the other atoms. Depending on what
you are actually trying to model, you might consider putting together an
appropriately sized fullerene to act as a sphere. What are you trying to
On Mon, 22 Sep 2003, AMIT PALIWAL wrote:
> Hi, Jim ...good to hear from you! regrading the specifics..i want to
> simulate a very large ( say a 5 or 10 ang. radius) hard sphere in water.
> Can i implement a step function type potential ( infinity if r < r0 and
> zero otherwise) ? I have never implemented spherical boundary conditions
> before...are their any examples anywhere? thanks, Amit.
> ----- Original Message -----
> From: Jim Phillips <jim_at_ks.uiuc.edu>
> Date: Monday, September 22, 2003 3:38 pm
> Subject: Re: namd-l: hard sphere simulation
> > I'd suggest modeling it as a very stiff "soft" interaction.
> > If you want a single sphere, substantially larger than an atom and
> > locatedat a fixed location then you can probably adapt the
> > spherical harmonic
> > boundary conditions code (src/ComputeSphericalBC.[Ch]) to implement
> > whatever hard-core potential (like (r-r_0)^(-12)) you want.
> > Otherwise, you'll need to be a little more specific in what you want.
> > -Jim
> > On Sat, 20 Sep 2003, Amit Paliwal wrote:
> > > Hi All,
> > > What is the best way to incorporate a hard sphere in a simulation?
> > > thanks,
> > > Amit.
> > >
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