On Wed, Aug 21, 2019 at 1:48 AM Erez Tamir <[email protected]> wrote: > > Dear all, > > I'm trying to perform IBI on polymer system contains 20 different molecules > (each molecule is a polymer chain). > The molecules differ by their structure, but they share the same bond and > angle types. I don't think that is something VOTCA supports, you can have multiple molecule of the same type with same bonds and angle, but different molecules types that share the same angle isn't something we had in mind when writing VOTCA.
Hence you will get the error below as the name "bond1-2" appears in multiple contexts. You could comment out this line: https://github.com/votca/csg/blob/master/share/scripts/inverse/functions_common.sh#L273 in your installation and see if the results look reasonable to you, but I am not guaranteeing anything. Also for bonded IBI, usually only a 1:1 mapping is required as the MD is already done on the CG level, but your the mapping file is an atomistic to cg one, so I am not 100% sure what your trying to do here. Christoph > I made different mapping file for each molecule, so in total I have 20 > mapping files. > I'm trying to divide each polymer chain to 30 coarse-grained beads. > I'm ussing LAMMPS dump files for trajectory. > When I perform IBI in order to get bonded potentials, this error message > appears: > > csg_get_interaction_property: cg_bonded name 'bond1-2' appears twice in > file(s) ... (list of all my 20 mapping files) > > 'bond1-2' represents bond between bead type 1 and bead type 2. > My settings file is attached together with one mapping file for example. > > I have seen other discussions about IBI on mixtures and I'm not sure if the > problem is my scripts or the votca versions I'm using (both 1.4 and 1.5-dev). > > I also tried to combine all my 20 mapping files into single molecule mapping > file, but then I face inconsistency with my trajectory file. > > Any help to overcome this issue would be appreciated > > Erez > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/c3488b63-7f74-4f3b-8c96-86cf11621ee9%40googlegroups.com. -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5iE4AwBPMw5D-KgjPWV%2BHmYnhbabvR5HE%2Bb4q%3DwWqZtw%40mail.gmail.com.
