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 On Mon, May 20, 2019 at 6:19 AM CHRISTINA-ANNA GATSIOU < [email protected]> wrote: > Thanks Christoph! That was very helpful! > > > On 20 May 2019, at 4:09 PM, Christoph Junghans <[email protected]> > wrote: > > > > On Mon, May 20, 2019 at 4:00 AM CHRISTINA-ANNA GATSIOU > > <[email protected]> wrote: > >> > >> 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. > > > > 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 [email protected]. > >> To post to this group, send email to [email protected]. > >> 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 > > > > -- > > 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 [email protected]. > > To post to this group, send email to [email protected]. > > 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/CAHG27e6rfMeN%2BroTG3pRp-DB8QoDuhqDKudj6mm-oesBMdK_gg%40mail.gmail.com > . > > For more options, visit https://groups.google.com/d/optout. > > -- > 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 [email protected]. > To post to this group, send email to [email protected]. > 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/B224A3FC-7B94-4C66-8053-3E05455AECCB%40gmail.com > . > For more options, visit https://groups.google.com/d/optout. > -- 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 [email protected]. To post to this group, send email to [email protected]. 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/CAH%2Bj%2BH%2B1NBDoFopgu8%3DVhR1oVcqKo%3DHZmK1TeDSsRmr_U%3DTuiA%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
