Your advice turns out to be very helpful! I wrote a topology .xml file and as a parameter passed it to --top, it worked very well, and finally generated the mapped RDF I want. Then I tested a hexane case which contains bonds and angles in the final CG configuraion, and in the end the CG angle/bonds were generated using csg_boltzmann. However, the distribution and the final bond/angle potentials are not so good as I expected. I guess there would need some extra efforts, maybe some smooth etc. Later I may use VOTCA to calculate CG potentials for some complex polymers, hope it will work as well. :P
Thank you for your help anyway! 在 2018年10月17日星期三 UTC+8下午8:39:31，Christoph Junghans写道： > > On Tue, Oct 16, 2018 at 9:43 PM <[email protected] <javascript:>> > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
