I just set it to one keeping in mind that with gromacs resid for second molecule also had to be 1. 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] <javascript:>> > 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] <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.
