Search found 2564 matches
- Thu Jan 25, 2024 1:11 pm
- Forum: OpenMM
- Topic: Recalculate forces on atoms
- Replies: 3
- Views: 2044
Re: Recalculate forces on atoms
I think it's just different units. You're printing the units in kcal/mol/nm. If you instead print them in kcal/mol/A they'll be 10 times smaller. That's probably what CHARMM is using.
- Tue Jan 16, 2024 10:38 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
I already said: all standard integrators apply constraints correctly. That correction is part of RATTLE. Other algorithms account for velocities in other ways, but all of them handle them correctly.
- Mon Jan 15, 2024 6:14 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
I don't understand your question. It is always applied. It's part of the algorithm.
All the standard integrators apply constraints correctly. They use different algorithms in which constraints come up in different ways, but each algorithm handles them in a correct way.
All the standard integrators apply constraints correctly. They use different algorithms in which constraints come up in different ways, but each algorithm handles them in a correct way.
- Mon Jan 15, 2024 9:33 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
SHAKE is a constraint algorithm. RATTLE is an integration algorithm. They're different because they do different things! Here's an implementation of RATTLE implemented with a CustomIntegrator. CustomIntegrator integrator(dt); integrator.addPerDofVariable("x1", 0); integrator.addUpdateContextState();...
- Sun Jan 14, 2024 10:05 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
Those algorithms are just different methods of solving the same system of equations. They all produce identical results (up to the tolerance you specify). The velocities are updated correctly in all cases.
- Sat Jan 13, 2024 11:07 pm
- Forum: OpenMM
- Topic: OpenMM 8.1.1
- Replies: 0
- Views: 725
OpenMM 8.1.1
8.1.1 is now released. You can install it with
Code: Select all
mamba install -c conda-forge openmm
- Sat Jan 13, 2024 5:55 pm
- Forum: OpenMM
- Topic: NetCDFReporter issue
- Replies: 2
- Views: 1074
Re: NetCDFReporter issue
Problems in ParmEd need to be reported at https://github.com/ParmEd/ParmEd/issues. I don't think the author reads this forum.
- Sat Jan 13, 2024 9:28 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
It depends on the platform, not on the integrator. All platforms use SETTLE for water. The Reference and CPU platforms use CCMA for everything else. The CUDA and OpenCL platforms use SHAKE for small clusters composed of hydrogens bound to a single heavy atom, and CCMA for anything else.
- Thu Jan 11, 2024 9:36 am
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
Correct, it would not.
- Wed Jan 10, 2024 8:16 pm
- Forum: OpenMM
- Topic: Constraints with Langevin Middle Integrator
- Replies: 14
- Views: 6614
Re: Constraints with Langevin Middle Integrator
Almost all integrators apply constraints at the level of positions, and possibly also velocities. You don't integrate the constraint forces. Instead you integrate as if there were no constraints, then modify the positions to satisfy the constraints. Based on how much they change, you can back-calcul...