I did run csg_map. The output gro file has the hexane molecules grouped into four CG particles as I indicated in the xml file, so looks like it is doing what I intended it to do.
On Thursday, 6 December 2018 10:49:21 UTC-5, Christoph Junghans wrote: > > > > On Wed, Dec 5, 2018 at 19:05 M. Chakraborty <[email protected] > <javascript:>> wrote: > >> The file just contains this comment without the actual exclusion list: "# >> atomistic: Protein cg: Protein cgmap: hexane.xml". I have also attached the >> mapping xml file that I am giving as an argument. I am using a four bead >> mapping scheme for hexane. >> > That usually means something is wrong in the mapping file! Try to run > csg_map first to see if your mapping file is doing what it is suppose to do! > > Christoph > >> >> >> On Wednesday, 5 December 2018 17:59:58 UTC-5, Christoph Junghans wrote: >>> >>> On Wed, Dec 5, 2018 at 11:41 AM M. Chakraborty <[email protected]> >>> wrote: >>> > >>> > Hello all, >>> > >>> > I am following the hybrid hexane example where the non-bonded >>> interactions are obtained by force matching and the bonded interactions are >>> obtained by Boltzmann Inversion. In hybrid_force_matching folder under both >>> the master and the stable branches, the discussion seem to be mostly on >>> getting the non-bonded interactions using force matching. I did not find >>> the part where BI is used to extract only bonded forces. I tried following >>> section 5.1 of the VOTCA manual which discusses the generation of exclusion >>> lists. However, using the csg_boltzmann command with the --excl tag did not >>> yield a list of exclusions of non-bonded interactions that it is supposed >>> to give. Could someone help me identify what I am missing here? Thank you >>> in advance! >>> What exectly went wrong with "csg_boltzmann --excl"? >>> >>> Yeah and there is another way to get the bonded interaction, starting >>> from the hexane/ibi_all example: >>> https://github.com/votca/csg-tutorials/tree/master/hexane/ibi_all >>> csg_inverse will do a Boltzmann inversion for all interactions >>> automatically in step_000, so you can just use these. >>> >>> Christoph >>> > >>> > >>> > -- >>> > 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. >>> > 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> Visit this group at https://groups.google.com/group/votca. >> 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. For more options, visit https://groups.google.com/d/optout.
