On Wed, Apr 17, 2019 at 4:05 AM <[email protected]> wrote: > > Hi, > > So I am trying to explore the LAMMPS functionality of votca. I have created a > propane water system and prepared all the necessary files but it does not > seem to be able to create the distributions. > I would be really grateful if you could explain how the xml files should be > in this case. I have attached the files I have prepared in order for you to > be able to point out the errors. > First you start with check if the atomistic topology is ok: $ csg_dump --top lammpsTopology.xml then you check the mapped topology: $ csg_dump --top lammpsTopology.xml --cg "cg_mapping.xml;pt_mapping.xml" There is an error: mapping error: molecule 1:Pt:C451 does not exist Looking back at the output from the first command, you will need to change 1:Pt to 2:Pt $ sed -i 's/1:Pt/2:Pt/g' pt_mapping.xml (I made an issue for that https://github.com/votca/csg/issues/369) Now let's calculated the distributions: $ csg_stat --top lammpsTopology.xml --cg "cg_mapping.xml;pt_mapping.xml" --options settings.xml --trj propane_water_eq.dump ....
written CG_CG.dist.new written Pt_CG.dist.new written Pt_Pt.dist.new Cheers, Christoph I don't know enough about data files, so Josh will have to answer that question. > Best regards, > Christianna > > ps. The attached is not a system to study and get meaningful results but > rather an example to understand how topology should be defined for > multicomponent system when using lammps. > > -- > 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.
