Write_data + read_data, delete atoms-error-input files attached

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,

  1. 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.
  2. 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.
  3. 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)


In data.ethane_delete file, number of dihedrals “432 dihedrals” in the top, and the number of dihedrals (423 dihedral lists) in “Dihderals” section are different.

When you change the number of dihedrals (432 -> 423) in the top of the data.ethane_delete file, it should work.


It may be also a bug of lammps which will not update properly the number of dihedrals in the top of data file associated with deleting atoms.


Thanks Chang Woong Jang. I am not comparing the dihedral lists section. Compare the number of dihedrals listed on the top of the two data files which I sent. They are the same. They should not be the same since I have deleted some atoms. The write_data command does not update dihedral information on the top of the data file after atom deletion.

Please try reading in data file using read_data command. It does not read. That is the problem
I have also tried editing the data file with the correct number of dihedrals which can be obtained from vmd/topotools.
Still I get an error reading in the data file.