Coarse-graining of water in confinement

[CHRISTINA-ANNA GATSIOU]

Hi, 

I have been trying to produce a CG force-field for a clay-water system (water confined in  a clay slit pore). Methods such as IBI does not really work for such systems. FM gave very poor results as well. I was wondering if VOTCA allows the use of alternative kind of distributions (instead of RDF, maybe Axial distributions) to perform IBI. Otherwise I would also be interested in any other methods that might work for such systems. 

Christianna

[Christoph Junghans]

There is slab IBI (https://github.com/votca/csg/issues/198), but it
never got merged.

Otherwise you can use a different distribution, you just have to
overwrite the script, which calculates with RDF (calc_rdf_generic.sh)
with something else.

In short, overwriting scripts works like this:
- make a new folder
- copy calc_rdf_generic.sh in there
- rename it my_rdf.sh (or something)
- create a file "csg_table" with a single line
rdf gromacs my_rdf.sh
in there. ("gromacs" should be replaced by the MD engine you are
planning to use.)
- add the path to the new folder to "scriptpath" option in your settings.xml
- modify my_rdf.sh to your needs

Christoph

>
> Christianna
>
> --
> You received this message because you are subscribed to the Google Groups "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to votca+un...@googlegroups.com.
> To post to this group, send email to vo...@googlegroups.com.
> Visit this group at https://groups.google.com/group/votca.
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/2338a850-db98-4378-9bc4-dedf9a19d733%40googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



--
Christoph Junghans
Web: http://www.compphys.de

[CHRISTINA-ANNA GATSIOU]

Thanks Christoph! That was very helpful!

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6rfMeN%2BroTG3pRp-DB8QoDuhqDKudj6mm-oesBMdK_gg%40mail.gmail.com.

[Sikandar Mashayak]

Hi Christina,

We were able to reproduce water density distribution in slit-like pore using relative entropy minimization method implemented in VOTCA. See the details in reference https://aip.scitation.org/doi/abs/10.1063/1.4769297

Regards,

Sikandar

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/B224A3FC-7B94-4C66-8053-3E05455AECCB%40gmail.com.