2017-08-11 9:28 GMT-06:00 <[email protected]>: > Hello, > I am new in Votca. I want to use IBI (csg_inverse --options settings.xml) > using the hexane tutorial files (both: ibi_all and also ibi_nonbonded), and > everything goes well, starting with the step_000 and then, in the step_001 > prepares everything to run the CG simulations with gromacs but, it gets > stucked and it is not going further. > > The last lines that it prints are about the grompp command > (from the inverse.log file) it says: > > csg_get_property: No value for 'cg.inverse.gromacs.log' found in > /work/sgerstenmaier/VOTCA/csg-tutorials-master/hexane/ibi_all/settings.xml, > trying /opt/share/votca-1.5-dev/share/votca/xml/csg_defaults.xml > csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log' > Running critical command 'mpirun -np 8 > /opt/share/gromacs-5.1.4/bin/gmx_mpi_d grompp -n index.ndx -f grompp.mdp -p > topol.top -o topol.tpr -c conf.gro' > > If I do out of vodca: > $gmx_mpi_d grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c > conf.gro > > it works properly generating the topol.tpr file. > > Do you know where is the problem? Thanks, thanks a lot, Looks good to me, so far. Can you try calling gmx grompp without mpirun, i.e. by setting cg.inverse.gromacs.grompp.bin to /opt/share/gromacs-5.1.4/bin/gmx_mpi_d grompp? grompp isn't really parallel....
Christoph > Susana > > -- > 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]. 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.
