From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 02 2012 - 20:56:09 CST
On Thu, Feb 2, 2012 at 9:20 PM, M.Raviprasad <M.Raviprasad_at_my.ndsu.edu> wrote:
> Hi Jim,
>
>
>
> This is regarding “repulsive/hard sphere simulation” posted long time ago.
> You mentioned in that post “ I'd suggest modeling it as a very stiff "soft"
> interaction”
>
>
>
> 1] What do you mean by Stiff “soft” interaction? If you could explain, that
> would be helpful.
that obviously means a lennard-jones interaction with a very large epsilon.
mind you that is not a very practical suggestion, since this would also
require to use a cutoff that is in the minimum of the potential (i.e.
very short)
and a very, very short time step. i suggest you read up on how hard
sphere potentials are handled in MD codes.
> 2] Say… system composed of few polymer chains and one oxygen atom as a hard
> sphere. How do I represent the oxygen atom as a hard sphere potential?
you cannot do a real hard sphere potential with a code like namd.
its integrator is not set up for that. are you sure that you don't
mean a repulsive-only soft potential? but a real hard sphere?
axel.
> Oxygen atom has to move within polymer system by having only kinetic energy
> like a hard ball]
>
>
> Thanks
>
> MRP
>
>
>
>
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:37 CST