# HADDOCK3 alascan hotspot criteria & model usage; and OpenMM GPU acceleration? on macOS

**URL:** <https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068>\
**Category:** HADDOCK\
**Tags:** haddock, support\
**Created:** [April 9, 2026, 3:59pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068 "2026-04-09T15:59:17Z")\
**Posts on this page:** 11\
**Page:** 1

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 9, 2026, 3:59pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/1 "2026-04-09T15:59:17Z")

</div>

Dear HADDOCK3 team,

I successfully installed and ran HADDOCK3 locally on macOS, and it works beautifully. Thank you for developing such a versatile and powerful framework; coming from an experimental training background, I’ve found HADDOCK extremely helpful in facilitating my research.

I have a couple of questions regarding the HADDOCK3-_alascan_ workflow and MD simulation:

1. **Alascan workflow:**  
What is the recommended cutoff for identifying hotspot residues? Is there a generally accepted threshold (e.g., Δscore \< -2 or -3), or should hotspots be defined statistically (e.g., as outliers beyond 1.5×IQR among interface residues within 5 Å)? I would appreciate guidance on best practices for interpreting these results. Additionally, there is a question regarding the number of models to run the alascan workflow. In the HADDOCK3 paper, only the top model is analyzed and shown, while the user manual indicates that multiple refined models are generated by a specified sampling factor.

2. **OpenMM / MD performance:**  
I managed to install OpenMM and it is correctly invoked within HADDOCK3 runs. However, I noticed that it appears to run on CPU only, making it significantly slower compared to standalone OpenMM usage on macOS, where GPU acceleration (e.g., via OpenCL platform specified) can be enabled.  
Is there currently a way to specify the OpenMM platform within HADDOCK3, or are there plans to support GPU acceleration in future releases?

At last, I would like to express my strong interest in potential future support for cryo-EM restraints to guide docking workflows in HADDOCK3, like webserver 2.4/2.5 ver..

Thank you again for your great work and support!

Best /Di

---

<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [April 10, 2026, 8:46am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/2 "2026-04-10T08:46:17Z")

</div>

Dear user,  
Thanks for your interest in using HADDOCK3 for your research.

1. In `[alascan]` module:

- we do not recommend any cutoff for identifying hotspot residues, but this rather give a qualitative appreciation of the potential residues that are important / specific for the interaction.
- Indeed, in the paper we only show the result for one model. But the module can be run on multiple models. If they **are clustered** , the results are averaged among cluster members.

1. `[openmm]` module:

- Usually, OpenMM detects by itself if the GPU is available (tested on Linux only), and should use it by default. It falls back on CPU mode if undetected. It probably means that it cannot by default detect the GPU on the MacOS. **_I will try to investigate_** , but I first need to find a MacOS with a GPU on it 🙂

1. Cryo-EM: It is planned to be added back to the code in the future, but I cannot yet announce any date.

---

<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [April 10, 2026, 8:53am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/3 "2026-04-10T08:53:58Z")

</div>

How did you enabled the GPU usage for OpenMM on your MacOS ?

---

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 10, 2026, 9:08am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/4 "2026-04-10T09:08:13Z")

</div>

Hi VGPReys,

After installing the openmm 8.5, i called out the platform in python script by running:

platform = Platform.getPlatformByName(“OpenCL”)

print(“Using platform:”, platform.getName())

Hope it help, it runs significantly faster then run haddock-openmm module through .cfg configuration.

Cheers

 ![Screenshot 2026-04-10 at 11.03.22](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/d/d5de7c4098b431c6075341f8249662f286a69785.png)

 ![Screenshot 2026-04-10 at 11.04.30](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/d/d89e27755847e331bf5909a9c68127100bd4894d.png)

 ![Screenshot 2026-04-10 at 11.04.16](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/7/7ca232b25b8a72f09a3e5403b4934e2619005d9a.png)

---

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 10, 2026, 9:19am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/5 "2026-04-10T09:19:33Z")

</div>

Hi,

Thanks for the clarification, and that makes sense. Initially, I was hoping for something more directly comparable to haddock suite tools like Spot-On, mainly to get clearer leads.

I also tried running _alascan_ on multiple models by first using the _mdrun_ module to generate refined structures from the top-ranked model. However, I noticed that the variation per-interface-residue is still quite high. I’m considering increasing the sampling factor (e.g., from 10 to 50) to see if the results converge better; does that sound like a reasonable approach to you?

Also, thank you for considering both OpenMM GPU support and future EM restraint incorporation; that would be fantastic to see. Really appreciate the continued development!

Cheers,  
Di

---

<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [April 10, 2026, 11:05am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/6 "2026-04-10T11:05:06Z")

</div>

I think it is a great idea to run an MD refinement before:

```toml
# ... something before
# Perform MD refinement
[mdref]
sampling_factor = 10 # for each input molecule, generate 10 MD runs
# If you only have 1 input molecule, you could increase this value

# Cluster them
[clustfcc]
# Run the alanine-scanning module
[alascan]

```

P.S.: `mdrun` does not exists but `mdref` 🙂

---

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 10, 2026, 12:10pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/7 "2026-04-10T12:10:08Z")

</div>

Ah, yes, mdref module! Thanks for the input, appreciated!

---

<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [April 14, 2026, 7:44am UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/8 "2026-04-14T07:44:30Z")

</div>

On my side, when I run the `[openmm]` module on MacOS, I get the following print in the logfile:

```auto
...
[2026-04-14 09:41:40,382 openmm INFO] Running on platform OpenCL
...

```

Could you please check that in your logfile too ?

---

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 14, 2026, 12:44pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/9 "2026-04-14T12:44:38Z")

</div>

Interesting… could that be the reason I built a new haddock image containing openmm and pdbfixer, so when I start running this new image haddock-openmm, it won’t take the GPU to work?

(base) ~ % nano Dockerfile.openmm

# _paster below in the Dockerfile and write out, enter, and exit the editor._

FROM haddock3

# _Install OpenMM + pdbfixer_

RUN python -m pip install --no-cache-dir openmm pdbfixer

# _build the new image:_

(base) ~ % docker build -f Dockerfile.openmm -t haddock3-openmm .

I assume your haddock is installed locally, so basically I need to install both in the same virtual environment like using conda command and it should work then?

---

<div class="post-metadata">

**Author:** ![DiT](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@DiT](https://ask.bioexcel.eu/u/DiT)\
**Post date:** [April 14, 2026, 1:16pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/10 "2026-04-14T13:16:32Z")

</div>

I got it to work now, using openCL; thank you very much!

[2026-04-14 15:11:47,702 openmm INFO] setting non-random seed = 918

[2026-04-14 15:11:47,702 openmm INFO] simulation seed 918 for complex\_haddock.pdb

[2026-04-14 15:11:48,042 openmm INFO] Running on platform OpenCL

[2026-04-14 15:11:48,042 openmm INFO] Estimated platform speed: 50.0

[2026-04-14 15:13:24,658 openmm INFO] Running NVT equilibration for complex\_haddock.pdb

---

<div class="post-metadata">

**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [April 14, 2026, 1:31pm UTC](https://ask.bioexcel.eu/t/haddock3-alascan-hotspot-criteria-model-usage-and-openmm-gpu-acceleration-on-macos/6068/11 "2026-04-14T13:31:10Z")

</div>

Super, nice to know you did it !  
On my side I used the [installation instructions on haddock3 using `venv`](https://github.com/haddocking/haddock3/blob/main/docs/INSTALL.md#in-venv)