I am aware of the force field specific to bond formation that is compatible with LAMMPS however, the system I am simulating alone is computationally taxing already and adding LAMMPS to my repertoire with a reactive force field would hinder my progression. Therefore, I am wondering if there is any advice anyone would like to share when manually adding new bonds during n steps of the simulation in any other molecular dynamics program.
Thanks
P.s. I am using Amber (atomistic) and Gromacs (coarse grain). LAMMPS is a last resort however I am open to the idea of using it to accomplish my task if there is not other way.
In classical MD simulations, bonds do not break or form. A reactive force field is the only way to handle such a case classically.
Your other options are:
1. QM/MM simulations, wherein the bonds can form within a QM subsystem. This is computationally very expensive.
2. After a certain interval of simulation, regenerate a topology for the existing coordinates with the formed bond and start a new simulation. Doing so naturally introduces a discontinuity that means you will have to re-minimize and re-equilibrate, because it is basically just a new system.
HI Justin,
Thank you so much for your input. I really appreciate it.
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