Minimum distance between two atoms in an MD run

Dear Julian,
I had run MD simulation at finite T, and watching the xyz output, I noticed that sometimes the distance between two atoms becomes unphysically too short. Can I constrain the minimum distance between two elements to d=R1+R2 where R1 and R2 are the “vdw” or “covalent” or “ionic” radii of elements 1 and 2? Or I had to do something else?
Thank you in advance.
Best regards,

Dear Mahmoud
There is a way to constrain a pair of atoms to be a rigid distance if it’s just 2 atoms, but this is the wrong way to approach things. If a model is giving unphysical answers then the solution is to fix the model. You need to examine the parameters for the interaction in question and work out why they are not keeping the atoms apart. You can then refit to QM data (for example) for a suitable interaction to ensure that the force field is sensible.
Best regards,


Hi Dear Julian.
Thank you so much for your quick reply and comment.
I will do as you suggested.

Kind regards,