Re: [ESPResSo-devel] Book-keeping of bonded partners

[Tristan Bereau]

Dear Christoph and Hanjo,

Thanks for your help.

The reason why I am not using a bonded potential is because I have
implemented a directional lennard-jones potential. That is, a product
of a LJ potential with angular dependence. This directionality is
provided by two bonded partners attached to each particle. So it's
really a non-bonded interaction, but I use the bonded partners to get
information about angular dependence.
I want to do this in order to recreate hydrogen bonds in a
coarse-grained fashion.
I thought I would find bonded partners in a dynamic way, but it
doesn't seem easy to do if the bond list is not communicated for
non-bonded interactions.

The alternative is probably to make sure my bonded partners have
particle IDs directly preceeding and following the main particle, but
this is by far not the best thing to do.

Thanks,

Tristan


On Thu, Apr 3, 2008 at 5:12 AM, Christoph Junghans
<address@hidden> wrote:
> Hi Hanjo,
>
>  you are right, for spring and angle etc it works.
>  I had the problem with rigid bonds, sorry for the confusion.
>
>  Bye,
>
>  Christoph
>
>  Limbach,Hans Joerg,LAUSANNE,NRC-FS schrieb:
>
>
>
> > Hi Christoph,
> >
> > Espresso does not "normally" crash setting up bonded interactions in
> > both direction! There is no reason for this behaviour.
> >
> > Reagrds,
> > Hanjo
> >
> > > -----Original Message-----
> > > From: address@hidden
> [mailto:address@hidden On Behalf Of Christoph
> Junghans
> > > Sent: jeudi, 3. avril 2008 09:12
> > > To: Tristan Bereau
> > > Cc: address@hidden
> > > Subject: Re: [ESPResSo-devel] Book-keeping of bonded partners
> > >
> > > Hi Tristan,
> > >
> > > some time ago I had the same problem. My solution is the following:
> > > -set up the real interaction between particle i and i+1.
> > > -set up a virtual bond between particle i+1 and i.
> > >
> > > Normally Espresso will crash, if you set up bonded interaction in both
> direction, but the virtual bond does nothing else than been in the bond
> list. No contribution to energy, pressure etc. You can imagine it as a
> spring with k=0, but without calculating the zero contributions.
> > >
> > > Is this what you need?
> > >
> > > Bye,
> > >
> > > Christoph
> > >
> > >
> > >
> > > Tristan Bereau schrieb:
> > >
> > > > Dear all,
> > > >
> > > > I am implementing a new non-bonded interaction that
> > > >
> > > requires knowledge
> > >
> > > > about bonded partners.
> > > > At the C level of Espresso, is there an easy way to
> > > >
> > > determine all the
> > >
> > > > bonded partners of a particle ?
> > > >
> > > > Say I have particles only connected by bond length
> > > >
> > > potentials (just an
> > >
> > > > example). If I take one particle (let's call it 'i'), I can get its
> bonded partner 'i+1' from the bond length, but not particle 'i-1'
> > > > (that's because it is particle 'i-1' that stores particle 'i' as a
> bonded partner).
> > > >
> > > > Right now I'm cheating by using the information given by
> > > >
> > > bond angles
> > >
> > > > between neighboring partners. Particle 'i' has a bond angle
> > > >
> > > with 'i-1'
> > >
> > > > and 'i+1'. This method works only if I use that
> > > >
> > > potential... Is there
> > >
> > > > any way I can do something more elegant ?
> > > >
> > > > As a side note, I get information about bonded partners by
> > > >
> > > using the
> > >
> > > > properties of particle i :
> > > > p_i+1 = local_particles[p_i->bl.e[...]]; I hope this is
> > > >
> > > what I should
> > >
> > > > be doing.
> > > >
> > > > Many thanks,
> > > >
> > > > Tristan
> > > >
> > > > _______________________________________________
> > > > ESPResSo-devel mailing list
> > > > address@hidden
> > > > https://fias.uni-frankfurt.de/mailman/listinfo/espresso-devel
> > > >
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> > > >
> > > >
> > > --
> > > Dipl.-Phys. Christoph Junghans
> > > Max Planck Institute for Polymer Research Theory Group POBox 3148 D
> 55021 Mainz, Germany
> > >
> > > Phone: +49 6131 379 335
> > > Web: http://www.mpip-mainz.mpg.de/~junghans
> > >
> > >
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> > >
> > >
> >
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>
>  --
>  Dipl.-Phys. Christoph Junghans
>  Max Planck Institute for Polymer Research
>  Theory Group
>  POBox 3148
>  D 55021 Mainz, Germany
>
>  Phone: +49 6131 379 335
>  Web: http://www.mpip-mainz.mpg.de/~junghans
>
>