If my understanding is correct, you should be able to pass the .data file in as a trjectory file and still specify the xml file as a topology file. The votca lammps parser automatically sorts the atoms based on their ids so it should not matter if they are out of order as long as they are associated with the correct atom id. You can refer to the csg manual, however not all use cases are in there and the lammps data reader is a relatively new addition. If you have been building votca from github using cmake you can build the manual by specifiying -DBUILD_CSG_MANUAL=ON flag with cmake, after you have installed the correct dependencies. https://github.com/votca/votca/blob/master/share/doc/INSTALL.md
Let us know if this helps, or not. On Tuesday, October 16, 2018 at 9:19:42 AM UTC-6, [email protected] wrote: > > Thank you for your efforts on this work! Actually I finally got the > up-to-date VOTCA worked a moment ago, and have tested some IBI iterations > using the spce lammps example. In this case, it just works well. However, > what puzzled me is that how can I write a mapping file like the > "hexane.xml" for lammps use, and to calculate the Boltzmann Inversion? > Because you know, in lammps data, all atoms are represented as numbers like > 1, 2 ... not so well-organized as in gromacs representations. Is there any > template or guide I can refer? > > Besides, is the --top parameter in commands like csg_boltzmann can just be > written as input.data? Considering that almost all such parameter in > examples are .tpr, so I wonder whether it could work ... > > Thanks :) > > 在 2018年10月15日星期一 UTC+8下午11:27:28，Joshua Brown写道： >> >> Hi, >> >> Also, if you have any trouble with the parser let us know, I implemented >> the lammps data reader but it has not been heavily tested. >> >> On Monday, October 15, 2018 at 5:23:52 AM UTC-6, [email protected] >> wrote: >>> >>> Hi, >>> >>> I am trying to use VOTCA to realize the Boltzmann Inversion method to >>> generate some bond or angle potentials. However, my equilibrium >>> configuration is calculated from LAMMPS. So I wonder whether I could use >>> directly the lammps data file or make a special xml file to accomplish my >>> goal? Or maybe make a bit modifications in the original codes? >>> >>> Thomas Meng >>> >> -- 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.
