Changing Bond Parameters During Run

Hi all,

I’m currently running into the need to change a default bond length on the fly, one that is regulated by shake (essentially I need to switch the position the atom is held at between two distinct states). I tried just using a second bond_coeff command between runs to change the bond parameters, but got out NaNs in the energies and general bad results.

The only other way I can think to possibly do what I want involves a complicated destruction of the existing bond and re-formation of a new one, and I was wondering if there was a less painful/involved way to manage this.

Thomas Allen
Makri Group

I think you need to write a custom fix to do this kind of constraint.

If you just want to change it once, between 2 runs,
you could add some code to the “set” command for (re)setting
a bond length. If you want to change it continuously during
a run, you could add some code to fix adapt to do that.

But as Axel said, you’re going to need to add code for that
new feature.