Hello,
I want to model polyethylene via LAMMPS. But, when I get run and visualize it through VMD, I see that the single structure shows as 3 separated structure with extra and undefined bonds. What is the problem with it? Does LAMMPS has bug about this structure?
I checked my data file, and it was correct.
I attached the files of data, input, and output of LAMMPS.
input.txt (508 Bytes)
Polyoxymethylene.lammps05 (16.6 KB)
Output .xyz (3.38 KB)
On iPhone now so short reply. (i can't download or check your attachments)
You should look at the starting structure (t=0) to see if it also has this problem. Don't just look at the tranectory for t>0.
There are messages on this mailing list discussing how to view the starting structure by loading your DATA file in VMS.
Search on google for a file named
README_visualize_vmd.txt
(I think)
It is also in this directory:
tools/moltemplate/CG_misc/translocation/
(In the lammps distribution)
Cheers
Andrew