Dear Lammps users, I am experimenting with a toy system constituted by 1024 water molecules (tip3p) confined in a
-25 25 xlo xhi
-30 30 ylo yhi
-30 30 zlo zhi
box and (for the moment) 1 p-phenylene diamine molecule in a
35 45 xlo xhi
-10 10 ylo yhi
-10 10 zlo zhi
box
Both systems were equilibrated with 300 ps NVT at 300 °K
I combined the two systems in one to test its proper functionality.
I got this message:
ERROR: Dihedrals defined but no dihedral types (src/read_data.cpp:1198)
Last command: read_data dat-PPDA-1-00 add append
I attach the input file and the PPDA data file
Any cvomment or diagnosis will be really welcome
Dear Paolo Botto ,
You forgot to attach the water data file. I think the following commands may help you.
read_data dat-PPDA-1-0 extra/atom/types 2 extra/bond/types 1 extra/angle/types 1
read_data dat-w-tip3p-1024-023 add append offset 4 4 5 1 1
.
.
run 1000
write_data combine.data
Considering dat-PPDA-1-0 data file as your first data file, and dat-w-tip3p-1024-023 as your second date file, which will be added to the first data file.
When you combine two data files, you must write the number of the atoms, bonds, angles, dihedrals and impropers of the second data file (e.g., dat-w-tip3p-1024-023 in this example) in the first read_data command, which will be added to the system later (e.g., extra/atom/types ...).
Then, in the second read_data command, in offset part (e.g. offset args = toff boff aoff doff ioff) you should write the number of atoms, bonds, angles, dihedrals and impropers of the first data file. Thus, in combine data file the id of atoms, bonds, … of second data file is equal to the id of first data file plus id of second data file. (For example, if the number of atoms in first data file is 4, and the number of atoms in second data file is 2. In combine data file the id of atoms of the second data file is 5 and 6).
However, there is an exception here. If there is not any dihedral or improper in the second data file, the doff and ioff args of offset should be 1.
Dear Saeed, I am very grateful to you for your detailed and clear explanation. I think you must be a very good person, since you devoted your time to patiently explain the correct procedure.
I am now in the process to update the files and make tests on larger systems.
Hope all the best to you and your family
Paolo
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