On Sat, Dec 26, 2020 at 4:29 PM nancyfor <[email protected]> wrote: > > Hello everybody, > > I am trying to get the probability distribution functions and the tabulated > potentials for a system with 11 coarse grained beads. However when listing > all available bonded interaction only list 3. Coincidentally, they are the > last bonded interactions for angle, bond and dihedral sections respectively. > I am using votca 1.6.2 and gromacs 2019.4 > > This is the output for > > csg_boltzmann --top topol.tpr --trj traj.xtc --cg mapping.xml > list > > Available bonded interactions: > molecule 0:EMBT:index 0 > molecule 0:MBT:index 0 > molecule 0:SMEMBT:index 0 > > I have checked if the mapping was correct using csg_dump, and it seems is > fine. > > I have attached the mapping file in case you spot any mistake. Yeah, you need to put each bond, angle, dihedral in its own <bond>, <angle>, <dihedral> block, otherwise all properties (name, beads etc) will be overwritten by the latest entry and hence you end up with one of each.
If the documentation is unclear on that, please modify the input_files.rst file in the share/doc folder of the csg module and send up as a patch or submit a pull request on GitHub. Christoph > Best regards, > Nancy > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > 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/561b4631-045c-45d6-b3b7-b9ee61646d4fn%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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/CAHG27e5ibXf%3DiOEBJu6e%3DvbDeg-Hui3%2BuxY-u_Ph%2B22nmMTa-w%40mail.gmail.com.
