nanodynamics-1 force field?

[Vlad]

Does anybody know the details of nanodynamics-1 force field used in NE1? What kind of interatomic potentials are used? Is it possible to break and restore bonds while applying linear motor  external force (to study the fracture of materials)? 

[Tom]

I believe the force field details were available on the wiki. However you can't really use the NE1 forcefield for anything you want to publish in a peer review journal as it has not been, shall we say, verified and accepted by the scientific community.

[prakhar gupta]

If I am not wrong is it Compass force field?

--
Prakhar Gupta

[Tom]

No. It was a forcefield developed by Nanorex.

[Bruce Allen]

If NanoEngineer uses GROMACS for MD simulations and GROMACS is using NanoDynamics-1 then I would say that it knows nothing about bonds breaking. I think it's fun to scrunck up a molecule so the atoms are very close and use a high temperature. The simulation shows all the atoms flying away from each other but the bonds are stretching forever into infinity.


-Bruce

[prakhar gupta]

Can we change the force field?..can we apply our own potential files?

--
*Prakhar Gupta

*
*Research Associate*
*Faculty of Engineering*
*Dayalbagh Educational Institute (DEI),Agra*
*India*
*
*
*www.dei.ac.in*

[Bruce Allen]

I'm sure it can be done. Keep in mind my last look the ND-1 told me it addressed bond, angle and Van der Waals? There are not
dihedral terms and no class II cross terms. The code has to be modified to handle a better force field or you can substitute different coefficients for the existing model.

[Eugen Leitl]

On Fri, Oct 19, 2012 at 08:53:20PM -0600, Bruce Allen wrote:
> I'm sure it can be done. Keep in mind my last look the ND-1 told me it
> addressed bond, angle and Van der Waals? There are not

Is the forcefield part Java, or C/C++?

--
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
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[Vlad]

It's the same that I saw. So I guess that the potential used in ND1 is a harmonic one (the stretching part), since after a huge stretching bonds start to recover their length

суббота, 20 октября 2012 г., 4:38:16 UTC+4 пользователь Godzilla1138 написал:

[Eugen Leitl]

On Sat, Oct 20, 2012 at 02:36:41AM -0700, Vlad wrote:
> It's the same that I saw. So I guess that the potential used in ND1 is a
> harmonic one (the stretching part), since after a huge stretching bonds
> start to recover their length

You need a toy forcefield for e.g. dragging and crude annealing, but
you also need a fine forcefield for checking structure stability,
including bond formation/dissociation. It doesn't have to be all
that realistic, since that would be computationally too expensive.

Way back I asked whether NE could run on a cluster, but today
it needs OpenCL support. That should give a very responsive system
on a modern high-end system. Of course, you still need clustering
(MPI) support for larger workloads.

> суббота, 20 октября 2012 г., 4:38:16 UTC+4 пользователь Godzilla1138
> написал:
> >
> > If NanoEngineer uses GROMACS for MD simulations and GROMACS is using
> > NanoDynamics-1 then I would say that it knows nothing about bonds breaking.
> > I think it's fun to scrunck up a molecule so the atoms are very close and
> > use a high temperature. The simulation shows all the atoms flying away from
> > each other but the bonds are stretching forever into infinity.
> >
> >
> > -Bruce
> >
> >
> > On Thu, Oct 18, 2012 at 11:07 PM, Vlad <justm...@gmail.com <javascript:>>wrote:
> >
> >> Does anybody know the details of nanodynamics-1 force field used in NE1?
> >> What kind of interatomic potentials are used? Is it possible to break and
> >> restore bonds while applying linear motor external force (to study the
> >> fracture of materials)?
> >
> >