On Tue, Oct 16, 2018 at 9:43 PM <[email protected]> wrote: > > Thanks! Just several minutes ago, I used a simple united atom propane case to > test. However, I still don't know how to set the cg_beads.beads section in > the .xml mapping file. In lammps, there isn't any residue name for a specific > kind of molecule. However the rule is "RESID:RESNAME:ATOMNAME", what is > RESNAME? These are just the bead names, you would use something like this: <beads> 1 2 3 </beads> You can see the names by running csg_dump: $ csg_dump --top system_nvt.data
However, it looks to me that the generated atom names in your data file aren't unique (Josh can we fix that?) and hence the bead sting above would be "1 2 1" and VOTCA won't be able to pick out the right atoms. I think your best option here to create an xml topology (see section 3.3 of the manual). > > And I attached the following files which I think to be necessary to call > functions like csg_stat. What are problems in them? Looking forward to your > reply. :P > > 在 2018年10月17日星期三 UTC+8上午3:48:14，Joshua Brown写道： >> >> 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 > > > 在 2018年10月17日星期三 UTC+8上午3:48:14，Joshua Brown写道： >> >> 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. -- 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.
