On Tue, Oct 16, 2018 at 1:42 PM Joshua Brown <[email protected]> wrote: > > 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. You should also be able to use the data file as topology input. The hexane.xml is a mapping file, which you unfortunately need to write by hand.
> 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 The latest version of the manual can also be found here: http://doc.votca.org/manual.pdf, no need to build it yourself. Christoph > > 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. -- 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.
