Visualize a polymer chain created by Pizza chain tool

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1

Hi all,

I use Pizza chain tool to generate a random polymer chain, and want to visualize it with VMD, but I don’t know what file format I should choose when I load the file. Can anyone tell me. Thank you very much.

Best,
Xujun

2

Hi all,

I use Pizza chain tool to generate a random polymer chain, and want to visualize it with VMD, but I don’t know what file format I should choose when I load the file. Can anyone tell me. Thank you very much.

This is more a VMD question than a lammps question and thus more suitable for the vmd mailing list. Yet in that case, you need to specify which kind of file you created. I assume it is a data file for use with the read_data command. In that case there is no direct support. You need to use the topotools plugin, which has support for reading lammps data files provided you provide the suitable atom_style.

Axel

3

If it is a data file, you can run it for 0 steps in LAMMPS and

produce a dump file that VMD reads directly.

Steve

4

Dear Axel and Steve,

Thank you for your answer. I have no experience with LAMMPS and even other MD softwares, but it sounds like the input file generated from Pizza chain tool cannot be visualized directly. Instead it has to be run in LAMMPS and dumped to another file for visualization. I will try it.

Xujun

5

Actually Pizza.py has a couple of viz options, like to an SVG file which

most browsers can view. Also an OpenGL based tool gl. However

for the latter you need to augment your Python with a few packages,

which can be tricky.

But those are poor substitues for something like VMD.

Steve