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Re: [ESPResSo] remove & change in bonded interactions

From: samira jamalian
Subject: Re: [ESPResSo] remove & change in bonded interactions
Date: Thu, 8 Apr 2010 17:26:34 +0430


Thanks a lot.
Is there any command to understand whether or not two particles are bonded?


On Thu, Apr 8, 2010 at 5:05 PM, Axel Arnold <address@hidden> wrote:

On Thursday 08 April 2010 13:20:39 samira jamalian wrote:
> Dear all,
> I am working on a system of particles which are bonded. I have 5000 bonds
> from one bonded interaction style. During my simulation, I need to remove a
> group of these bonds. How could I do that?

part 10 bond delete 0 11

deletes a bond of type 0 to particle 11 from particle 10. That is, you need to
know what bonds you need to delete, and with which particle you defined them,
then you can delete them by using the same command as setting them, just with
the additional keyword delete.

part 10 bond delete

will delete all bonds registered with particle 10.

> I have another question:
> Assume that you have a harmonic potential:
> *inter 10 harmonic $K $R*
> I want to change the R of a special bond during my simulation.  If I
> define: *
> inter 10 harmonic $K $R_new*
> Would it be overwritten on the old one?

Yes. You can also change the type of bond, but not from harmonic to e.g.
angular, since then you don't have the right number of bonding partners.


Dr. Axel Arnold Tel: +49 711 685 67609
ICP, Universität Stuttgart      Email: address@hidden
Pfaffenwaldring 27
70569 Stuttgart, Germany

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