Hi Christoph, thanks a lot, the installation had actually problems. The administrator of the cluster reinstalled and now it is working :) S.
On Friday, 11 August 2017 20:35:57 UTC+2, Christoph Junghans wrote: > > 2017-08-11 9:28 GMT-06:00 <[email protected] <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
