delete atom???

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1

Hi
I tried to delet some extra water molecules after nvt run. I build a regien and then use this commend : delete_atoms region 1
But i i receive this error:

Bond atom missing in image check

I’m sure this error is because of delete commond, but I don’t know how can i solve it???

2

Hi
I tried to delet some extra water molecules after nvt run. I build a regien
and then use this commend : delete_atoms region 1
But i i receive this error:

Bond atom missing in image check

I'm sure this error is because of delete commond, but I don't know how can
i solve it???

you delete atoms, but you didn't delete the bonds associated with it.
in fact, you should not simply delete individual atoms, but rather
entire molecules. this is possible with the very latest patch level of
LAMMPS (where these features are available), or it needs to be done
with an external program.

axel.

3

Thanks axel

You mean that I should use both delete-atom command and delete-bonds command?

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4

Thanks axel

You mean that I should use both delete-atom command and delete-bonds
command?

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​no.​
​

5

See the mol option for the delete_atoms command
in current LAMMPS.

Steve