Search found 8 matches
- Tue Jan 16, 2024 12:06 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
Thanks for your patience and help, I learned a lot from this!
- Mon Jan 15, 2024 7:04 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
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?
- Mon Jan 15, 2024 2:01 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle 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...
- Mon Jan 15, 2024 8:22 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
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 ...
- Sun Jan 14, 2024 7:17 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
So you never satisfy the velocity constraints in a simulation (unless its water)? Does that not create artifacts?
- Sat Jan 13, 2024 7:03 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
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...
- Thu Jan 11, 2024 7:35 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Re: Constraints with Langevin Middle Integrator
Thanks, that makes sense! So if I were to dump forces would it not include the constraint forces?
- Wed Jan 10, 2024 6:55 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6530
Constraints with Langevin Middle Integrator
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...