From: M.Raviprasad (M.Raviprasad_at_my.ndsu.edu)
Date: Thu Feb 02 2012 - 22:18:23 CST
My intention is to study the movement of "Particles" in the polymeric system. This particle has mass and radius. It does not interact with polymer through Electrostatic or Van der Waals interaction however It moves within polymer by having only kinetic energy. We would like to observe the movement of this particle during some period of time. Since we are using NAMD for our simulations we discard the idea of using real hard sphere potential. However, we would like to use repulsive-only soft potential.
In order to use this set-up , can we use very small epsilon value to make it only repulsive?
Any other way to accomplish this?
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: Thursday, February 02, 2012 8:56 PM
Subject: Re: namd-l: Hard sphere potential
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"
> 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.
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?
> Oxygen atom has to move within polymer system by having only kinetic
> energy like a hard ball]
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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