2013/6/3 Hossein Motevaselian <[email protected]>:
> Hi,
>
> I am trying to coarse grain a mixture with two distinct molecules in a
> graphene silt confinement, using IBI scheme.
> I have prepared the setup and run the simulations for 300 iterations using
> 300ps md simulation in each of them. However,
> RDF plots of IBI is showing fluctuations in fluid-fluid and wall-fluid RDFs
> (for wall-fluid RDF, the fluctuations are intense).
>
> I was wondering if this is related to the issue that mentioned in VOTCA
> paper ( J. Chem. Theory Comput., 2009, 5 (12) )
> regarding the stability issues of IBI for multicomponent systems. And is
> this "multicomponent" terminology just for systems
> with internal degree of freedom or it also includes mixtures of molecules
> assuming no internal degree of freedom within the molecule?
Maybe, but this is really system dependent and I, personally, never
found a problem with IBI of multi-component systems.
It might help to play with the update sequence in do_potential. (see
the propane example). I recommend to only update one potential at the
time.
>
> You also mentioned in your paper that the scheme can be stabilized by
> multiplying the update function, DeltaU, by a factor eta[0..1].
> Is there any way to introduce this factor in the script shells for just IBI
> scheme?
Add something like:
<post_update>scale</post_update>
<post_update_options>
<scale>0.1</scale>
</post_update_options>
to the cg.non-bonded block of the interaction you want to scale.
Cheers,
Christoph
>
> Thank you so much in advance.
>
> Bests,
> Hossein
>
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>
--
Christoph Junghans
Web: http://www.compphys.de
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