Re: Hard sphere potential

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 02 2012 - 22:41:22 CST

On Feb 2, 2012, at 11:18 PM, "M.Raviprasad" <M.Raviprasad_at_my.ndsu.edu> wrote:

> Hi,
> 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?

No. You *really* should spend some time on improving your
understanding of the fundamentals of force fields.

> OR
> Any other way to accomplish this?

To make a repulsive only potential you have to either pick a
functional form that has no minimum or take a potential that has an
attractive branch and place the cutoff in the minimum of the
potential. You'll have to carefully read the manual to see what would
be an option to do that. Possibly you'll have to write a tclforces
script for it.

Axel

>
> Thanks
> MRP
>
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Thursday, February 02, 2012 8:56 PM
> To: M.Raviprasad
> Cc: namd-l_at_ks.uiuc.edu
> 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"
>> 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.
>
>

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