Thank you for considering the issue Dr. Axel and steve. I am using the latest version of lammps (august 15). I am attaching the input script file (in.step2b) and the data file (data.step2b). These are from Dr. Axel’s website (ethane example). This what I did,
- Ran the input script, which simulates ethane in the nve ensemble with the group, delete atoms and write_data line commented and made sure the script ran without any errors.
- uncommented the the three lines which contain the group, delete atoms and write_data lines in the input script and ran the script. The new data file name is data.ethane_delete.
- The original data file has 432 dihedrasl (data.step2b). The new data file after deletion of atoms also has 432dihedrals.
but according to topotools/vmd it should have only 423 dihedrals.
and also try reading the data file using the read_data command. It does not read.
I have attached the input script and the datafile. Please have a look.
Dr. Axel what did mean when you said you are not able to reproduce ?. Did you get the right number of dihedrals ?
Does this patch resolve the issue with the dihedrals ?
As Dr. steve said I do not know whether its my mistake or lammps mistake.
If it is my mistake please give suggestions on how to make it work.
data.ethane_delete (90.4 KB)
data.step2b (43.5 KB)
in.step2b (889 Bytes)