Dear GROMACS users

I noticed my ligand has some broken bonds and changes in atoms arrengement 
after md simulation was done. I have read before that no bond is broken and 
created in simulation . So why have been ligand changed ? 
I think, i have to notice that when i wanted to create a ligand topology , i 
used ATB server to create topology and pdb files. and when wanted to reassign 
the charges and charge groups, noticed that some of the atoms of ligand that 
have to be in a charge group, were not successive  , so decided to rearrange 
them and replaced them to place them in a charge group. 
I dont know if it is possible the brocken bonds in the ligand after simulation 
for 1 ns because of its topology?I am using gromacs 2016.3 and gromos96 54 a7 
ff.


thanks in advanceTavakoli

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