2013/9/18 Scott Sides <[email protected]>: > Christoph, > > I'd like to run the propane example with lammps (I've managed to get the > spce example running and its very informative). > I've looked at the lammpsreader.cc page you've listed in other posts. I was > wondering if you could give a quick outline of steps > needed to bring the propane example up to speed with lammps. Start from the gromacs inputs (propane/ibi). Besides the lammps input files, you will need a topology.xml like this: <topology base="conf.gro"> <box xx="4.96337" yy="5.13917" zz="4.52386"/> <molecules> <clear/> <define name="Protein" first="1" nbeads="3" nmols="1000"/> </molecules> <beadtypes> <rename name="A1" newname="A"/> <rename name="A2" newname="A"/> <rename name="B1" newname="B"/> <mass name="A" value="15.035"/> <mass name="B" value="14.027"/> </beadtypes> </topology>
The <beadtypes> block is not 100% necessary. Instead of renaming the beads you could also change the settings.xml file using type "A*" instead of "A" and "B*" instead of "B" in the type file of the different interactions. Correct mass values are not needed for IBI, but lets do it right, so that we don't forget it later. Cheers, Christoph > > > thanks, > Scott W Sides (NREL) > > -- > 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/groups/opt_out. -- 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/groups/opt_out.
