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Coarse-graining potentials from atomistic references made easy
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Error during IBI csg Tutorial of liquid Hexane #590

Closed mangesh-bhendale closed 4 years ago

mangesh-bhendale commented 4 years ago

I am trying to perform Hexane tutorial. I finished the atomistic simulation of hexane and got the A-A, A-B, B-B rd's and bond and angle distribution also. Now, while I am trying to to the IBI coarse graining an occurred and this was mentioned in the onverse.log file:

For a more verbose log see: inverse.log csg_get_property: No value for 'cg.inverse.mpi.tasks' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.tasks' csg_get_property: No value for 'cg.inverse.mpi.cmd' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.cmd' csg_get_property: No value for 'cg.inverse.parallel.tasks' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.tasks' csg_get_property: No value for 'cg.inverse.parallel.cmd' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.cmd' csg_get_property: No value for 'cg.inverse.gromacs.mdrun.bin' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.bin' csg_get_property: No value for 'cg.inverse.espresso.bin' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.bin' csg_get_property: No value for 'cg.inverse.scriptdir' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.scriptdir' csg_get_property: No value for 'cg.inverse.gromacs.grompp.topol' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.topol' csg_get_property: No value for 'cg.inverse.gromacs.grompp.index' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.index' csg_get_property: No value for 'cg.inverse.gromacs.g_rdf.topol' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.g_rdf.topol' csg_get_property: No value for 'cg.inverse.convergence_check' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check' csg_get_property: No value for 'cg.inverse.convergence_check_options.name_glob' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.name_glob' csg_get_property: No value for 'cg.inverse.convergence_check_options.limit' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.limit' csg_get_property: No value for 'cg.inverse.espresso.table_end' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.table_end' csg_get_property: No value for 'cg.inverse.gromacs.traj_type' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.traj_type' csg_get_property: No value for 'cg.inverse.gromacs.topol_out' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml

I checked the settings.xml file; but above mentioned things are not present there. I am unable to understand the error.

Please help.

junghans commented 4 years ago

On Tue, Sep 1, 2020, 03:52 mangesh-bhendale notifications@github.com wrote:

I am trying to perform Hexane tutorial. I finished the atomistic simulation of hexane and got the A-A, A-B, B-B rd's and bond and angle distribution also. Now, while I am trying to to the IBI coarse graining an occurred and this was mentioned in the onverse.log file:

For a more verbose log see: inverse.log csg_get_property: No value for 'cg.inverse.mpi.tasks' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.tasks' csg_get_property: No value for 'cg.inverse.mpi.cmd' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.mpi.cmd' csg_get_property: No value for 'cg.inverse.parallel.tasks' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.tasks' csg_get_property: No value for 'cg.inverse.parallel.cmd' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.parallel.cmd' csg_get_property: No value for 'cg.inverse.gromacs.mdrun.bin' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.mdrun.bin' csg_get_property: No value for 'cg.inverse.espresso.bin' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.bin' csg_get_property: No value for 'cg.inverse.scriptdir' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.scriptdir' csg_get_property: No value for 'cg.inverse.gromacs.grompp.topol' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.topol' csg_get_property: No value for 'cg.inverse.gromacs.grompp.index' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.grompp.index' csg_get_property: No value for 'cg.inverse.gromacs.g_rdf.topol' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.g_rdf.topol' csg_get_property: No value for 'cg.inverse.convergence_check' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check' csg_get_property: No value for 'cg.inverse.convergence_check_options.name_glob' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.name_glob' csg_get_property: No value for 'cg.inverse.convergence_check_options.limit' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.convergence_check_options.limit' csg_get_property: No value for 'cg.inverse.espresso.table_end' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.espresso.table_end' csg_get_property: No value for 'cg.inverse.gromacs.traj_type' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml csg_get_property: returning emtpy value for 'cg.inverse.gromacs.traj_type' csg_get_property: No value for 'cg.inverse.gromacs.topol_out' found in /root/votca/csg-tutorials/hexane/ibi_all/settings.xml, trying /share/votca/xml/csg_defaults.xml

I checked the settings.xml file; but above mentioned things are not present there. I am unable to understand the error.

There aren't errors, it just means there is no default value for these properties.

What are the last couple of lines before the error message? Or attach the whole inverse.log here.

Christoph

Please help.

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mangesh-bhendale commented 4 years ago

Yes, I did not find any default values of those parameters. Where can I find them?

I am attaching the inverse.log file here. inverse.log

junghans commented 4 years ago

On Tue, Sep 1, 2020 at 07:29 mangesh-bhendale notifications@github.com wrote:

Yes, I did not find any default values of those parameters. Where can I find them?

I am attaching the inverse.log file here.

inverse.log

If you look at the very end it says “gmx_d grompp” failed and if you scroll a bit up

Fatal error: The group cutoff scheme has been removed since GROMACS 2020. Please use the Verlet cutoff scheme.

In short, to do coarse-graining you basically need to use gmx-2019.* (or lammps) as the current gromacs version has no support for tabulated interactions. (see and comment on https://gitlab.com/gromacs/gromacs/-/issues/1347)

Cheers,

Christoph

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junghans commented 4 years ago

A warning was added a while back to CMake in #452.