Re: [votca] Topology does not have beads of type, which was specified in type1 of interaction "*-*"

[Christoph Junghans]

On Mon, Sep 11, 2023 at 10:04 AM Ran Zhao <ranzh...@gmail.com> wrote:

Dear all:

        

           I am currently using VOTCA to do an IBI process for a single polymer based on a dataset obtained from the experiments and utilizing LAMMPS to perform molecular dynamic simulations. 

           After all the preparations, VOTCA successfully performed the first step of the iterative Boltzmann inversion. But when VOTCA is ready to start the second step of the inversion, there is an error when using the csg_stat command to invert the non-bonded potential, As shown in the figure below.

I then realized that I didn't give the atom types special character names in the LAMMPS topology file (lammps.data). As far as I know, it doesn't seem to be possible to name atom types by a string in LAMMPS topology file. 

I refer to the example given in csg-tutorial file (spce water: ibi_lammps), the atom type of CG water beads in the topology file is "1", and there is <type1>Bead1</type1>  in settings.xml. I also changed this to Bead1 in my settings.xml file, but there is still an error!

Then, I just write "1" in the settings.xml file, but this error still exists.

I've been plagued by this error for days. Hopefully, I can get some help from you!

You can just run "csg_dump --top <your topology_file>" to see what votca reads. If the lammps topology doesn't work for you, you can alternatively create an xml topology file.

Christoph

Yours sincerely

Boran Zhao

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Christoph Junghans
Web: http://www.compphys.de

[Ran Zhao]

Hello,  Christoph:

Thank you for your enthusiastic help. I will try this out.

Additionally, due to improper expression, I just deleted this post and made the necessary modifications to post it again.

Best

Boran Zhao