Just to be clear if the lammps data file for two water molecules has two water molecules with the atoms arranged like this (pseudo data):
4 x-pos y-pos z-pos 3 x-pos y-pos z-pos 6 x-pos y-pos z-pos 2 x-pos y-pos z-pos 5 x-pos y-pos z-pos 1 x-pos y-pos z-pos After the parser reads the data in it will be stored internally as: 1 x-pos y-pos z-pos 2 x-pos y-pos z-pos 3 x-pos y-pos z-pos 4 x-pos y-pos z-pos 5 x-pos y-pos z-pos 6 x-pos y-pos z-pos As long as the atom 1 and the atom 3 are associated with the Oxygens and the 2, 3, 5, 6 atoms the hydrogens you can still use the .xml file for mapping purposes, becuase there is a pattern after the atoms have been ordered according to their atom ids. On Tuesday, October 16, 2018 at 1:42:16 PM UTC-6, Joshua Brown 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. > 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.
