Can you send the tpr file as well? On Sun, Dec 27, 2020 at 05:01 nancyfor <[email protected]> wrote:
> The rest of the files: > > I have also check the exclusions with the csg_dump, again with the > different versions. Using > > csg_dumpp --top mma_trimer_sd_noexclusions.tpr --excl > > I got the same output for the three cases. > > Not sure what is happening. > Cheers > Nancy > On Sunday, 27 December 2020 at 12:56:05 UTC+1 nancyfor wrote: > >> Hi Christoph, >> >> I have corrected the mapping file. However, when creating the >> exclusion.txt I noticed this file was not correct. For this I generated a >> .tpr file without exclusions >> and use: >> >> csg_boltzmann --top mma_trimer_sd_noexclusions.tpr --cg >> mma_trimer_mapping.xml --excl exclusions.txt >> >> I used votca 1.6.2. I tried two other versions of votca, sourcing >> someone else installation, votca 1.6-dev and a local machine version. >> >> I supposed this is a problem with my installation. Is there a way to >> check that votca was installed correctly? I did not get any error while >> installing it. And I have not seen anyone with this problem browsing the >> messages. >> >> I have attached the mapping file and the exclusion files for the >> different votca versions. >> >> details of the versions below >> >> csg_boltzmann, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, >> 15:56:40) >> votca_tools, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:55:42) >> gromacs, 2019.4 (single precision) >> >> >> csg_boltzmann, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, >> 17:41:20) >> votca_tools, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, >> 17:40:52) >> gromacs, 2019.4 (single precision) >> >> >> csg_boltzmann, version 1.5 (compiled Feb 8 2019, 02:59:36) >> votca_tools, version 1.5 (compiled Feb 8 2019, 02:57:53) >> gromacs, 2019.1 (double precision) >> >> On Sunday, 27 December 2020 at 10:18:45 UTC+1 nancyfor wrote: >> >>> Thanks Christoph, I completely overlooked this. >>> Cheers, >>> Nancy >>> >>> On Sunday, 27 December 2020 at 01:23:11 UTC+1 Christoph Junghans wrote: >>> >>>> 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/58e38a35-6a98-422f-8282-c02f2c7f95c8n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/58e38a35-6a98-422f-8282-c02f2c7f95c8n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAHG27e775B92qzT2zGJ6HBVa%3Drv2xnCQfZH7km8J%2B7iv8jiUTw%40mail.gmail.com.
