Thanks for your patience and help, I learned a lot from this!

Oh, you said that the (x1 - x)/dt correction is part of RATTLE and not the constraint algorithm (SHAKE, CCMA etc.). I was asking if that correction is used by OpenMM when you use a constraint algorithm or do you have to define a custom integrator?

Why would you not always need to apply that velocity correction though? It seems that the forces used in the position update should always be the same ones used in the velocity update. And within OpenMM is this correction added when you use constraints automatically or do you have to define a custom...

Well we're far beyond my original question, so now I'm just trying to understand. The systems of equations for RATTLE and SHAKE are different though, and looking at the CCMA paper it looks like you only solve the equations generated by the position constraints. In integration schemes where you also ...

So you never satisfy the velocity constraints in a simulation (unless its water)? Does that not create artifacts?

Another quick question on constraints. Which algorithms are used internally by OpenMM when constraining a simulation? Reading the docs it sounds like you use SETTLE for water, but otherwise does it depend on the integrator chosen? Like for LangevinMiddleIntegrator is only SHAKE used whereas for Velo...

Thanks, that makes sense! So if I were to dump forces would it not include the constraint forces?

Hello, I was reading through the integrators section and was curious to learn more about how the constraints are implemented in the LangevinMiddleIntegrator (as I am trying to code it myself). From my understanding algorithms like SHAKE and RATTLE add "constraint forces" to the existing inter atomic...