On Wed, Apr 17, 2019 at 8:00 AM <[email protected]> wrote: > > I just set it to one keeping in mind that with gromacs resid for second > molecule also had to be 1. Yeah, there are some inconsistencies between the different readers.
Christoph > Thank very much for your help > > On Wednesday, April 17, 2019 at 3:52:39 PM UTC+3, Christoph Junghans wrote: >> >> 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. -- 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.
