I merge two data file and make one data file and I deleted overlap atoms by command "delete atom " and with mol yes option to delete the whole of the overlapped molecule.
when I run the simulation I get a "Bond atom missing in image check " error .
how can I resolve the problem?
Most likely something went wrong during the merging process. How did you merge?
I merged them with attached input file .
the first data file has 8 atom type and some bond angle etc .
the second one has only two atom type and no bond or angle (a nanotube)
merge.in (313 Bytes)
please note how read_data add can modify your box dimensions.
if you have nonzero image flags for some atoms in either data file, that will also result in displacing those atoms in an undesired way.
it is therefore advisable to adjust your box without displacing atoms using change_box beforehand to avoid this undesired side effect.
THANK YOU PROF.KOHMEYER FOR YOUR REPLY
but two simulation box is the same and simulation box of the merged data file is exactly the same as them.
I deleted the “delete atom” command and error resolved. but the nanotube exploded (because of overlapping ).
It seems the error is because of “delete atom” command not properly set.
i have no advice for that. if you construct a bad geometry, bad things happen. that is just physics. you need to generate a better geometry then and not delete atoms that have bonds.