Hi, 2015-05-25 21:40 GMT-06:00 Tonalli Rodríguez <[email protected]>: > Hello developers and users, > > > I am new to votca package, I have installed the development version, and I > am using LAMMPS as simulation program. I want to use votca in order to > obtain optimize force fields. I have tested spce/ibi, spce/ibi_lammps, and > spce/simplex. I have tried to modify spce/simplex using the files > CG-CG.dist.tgt, conf.gro, index.ndx, and topol.top from spce/ibi, I have > modified the settings file. Everything seems to be ok in the first steps > and then I got this: > > step 9 done, needed 80 secs > > Doing iteration 10 (dir step_010) > > Simulation with gromacs You are still using gromacs and not lammps. Is that what you want?
> > Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated > interactions only work with Group cutoff-scheme! > > ####################################################################################### > > # > # > > # ERROR: > # > > # run_gromacs.sh: There is a nan in 'confout.gro', this seems to be wrong. This error means that one of the coordinates in the output file (confout.gro) is undefined (nan= Not a number). For the simplex optimization this is not uncommon as an Expansion move can bring you into undefined territory. I recommend using a pre-simulation to minimize the coordinates first as done in the spce/simplex example (see the grompp.prep.mdp file in there). > # > > # For details see the logfile > /scratch/tonalli/simulaciones/csg-tutorials/spce/simplex_bulk/inverse.log # > > # > # > > ####################################################################################### > > > Thanks, > > Tonalli > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
