I want to understand these things in both intuitive and non-intuitive ways. In some cases, we constrain hydrogens so that we can run molecular dynamics at a higher time step than we normally would, also tricks like using virtual sites. I can understand that these tricks allow us to propagate our system so that it becomes computationally stable. Non-bonded interactions shouldn't be affected by these, but what about the bonded interactions and eventual dynamics. Won't it affect the eventual dynamics of the system, also some properties of the system. I hope I made my question clear. If not, I can elaborate more. Thanks.
↧