2017-08-14 3:05 GMT-06:00 <sufigueroa0...@gmail.com>: > Hi Christoph, thanks a lot, > the installation had actually problems. The administrator of the cluster > reinstalled and now it is working :) > S. Thanks for the update.
> > On Friday, 11 August 2017 20:35:57 UTC+2, Christoph Junghans wrote: >> >> 2017-08-11 9:28 GMT-06:00 <sufigue...@gmail.com>: >> > 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
