2017-08-24 8:40 GMT-06:00 <[email protected]>: > Hello votca users, > > I'm trying to create topology and mapping files for coarse-graining polymer > system with various molecule types (i.e. chains with variuos length and > chemical structure). > > I'm using atomistic lammps trajectory or .pdb files as basis. > > Would anyone advise what should be the correct form of topology and mapping > files for such system? Have a look at the manual: doc.votca.org/manual.pdf, section 3.1 for the mapping and section 3.3 for xml topology file (which will work best with LAMMPS).
And I would start with a single repeat unit of the polymer. If the unit isn't too big you can use the stock tool http://stock.cmm.ki.si/smt/ interactively. Christoph > > Regards, > Erez > > -- > 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.
