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Hi !
I am a newbie, I am trying to find some tools to do QM/MM or QM/MM MD with protein and Small molecules.
I think maybe i can use ORCA&Chemshell&some MD software.
But today i find your ASH.
C…
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I've been thinking about refactoring the `initialize` and `address_finder` code to make it easier to test, fully migrate to goblin where we can (#50), etc. py-spy has a cleaner and more mature solutio…
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1. `发生异常: NameError
name '_SPLITS_COCO5_FORMAT' is not defined
File "/home/cv/yj/5.semi-object/OneTeacher-main/data_processing/builtin.py", line 103, in register_coco5
for _, splits_per_datas…
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We are currently working on obtaining free energy information for a large protein complex using a coarse-grained Martini model in OpenMM. However, we've encountered challenges in aligning our calculat…
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Steps to try to create a FZ with high-symmetry borders:
1. Analytically define cusps and sample cusp points OR sample cusp locations by numerically differentiating BRK function (2nd derivative) and u…
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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Hi!
When trying to run a basic umbrella sampling simulation with mace_mp0 the quench function does not seem to update the starting point of the walkers.
```
mace_mp0_small = MACEHamiltonian.mace_…
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I am opening this thread to coordinate contributions to new tutorials for use in the OpenMM 8 paper.
I'll keep this list updated with the discussion below:
- [ ] Extend `openmm-cookbook` to build …
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I am encountering problems in the dynamics of my system due to massless atoms.
As found before by #2113 the system energy explodes when two atoms overlap even if one is massless and has no LJ site, …