quick fix openm install and 8.2 version

docs/INSTALL.md

@@ -89,17 +89,41 @@ information.
 
 ## `openmm`
 
-1. Install the latest version of openmm and pdbfixer
+The use of the openmm module requires the installation of both OpenMM and pdbfixer.
+
+### In venv
+
+The venv installation instruction uses `pip` and requires a python version >=3.10 (not functional with python3.9).
+
+```bash
+# Create a new virtual env
+python3.12 -m venv hd3-openmm
+source hd3-openmm/bin/activate
+# Install haddock3
+pip install .
+# Install OpenMM
+pip install openmm
+# Install openmm - pdbfixer
+pip install https://github.com/openmm/pdbfixer/archive/refs/tags/v1.10.tar.gz
+```
+
+### In conda
+
+The Conda installation instructions are using conda-forge to retrieve packages and requires a python3 version between 3.9 and 3.12.
+
 ```bash
+conda create -n hd3-p39-openmm python=3.9
 # Activate the haddock3 env
-conda activate haddock3
+conda activate hd3-p39-openmm
+# Install haddock3
+pip install haddock3
 # libstdxx must be installed, maybe already present in your system
 conda install -c conda-forge libstdcxx-ng
 # Install OpenMM and related tools/binaries
-conda install -c conda-forge openmm pdbfixer
+conda install -c conda-forge openmm==8.2.0 pdbfixer
 ```
 
-Openmm should automatically detect the fastest platform among those available
+OpenMM should automatically detect the fastest platform among those available
 on your machine.
 
 Please refer to the [official page](http://docs.openmm.org/latest/userguide/)

src/haddock/modules/refinement/openmm/__init__.py

@@ -98,26 +98,17 @@ def confirm_installation(cls) -> None:
         ThirdPartyIntallationError
             When OpenMM pdbfixer is not installed
         """
-        def run_subprocess(command_to_run: str) -> str:
-            """Run subprocess."""
-            subprocess_output = subprocrun(
-                [command_to_run],
-                shell=True,
-                capture_output=True,
-                encoding='utf-8',
-                )
-            return subprocess_output.stdout.strip()
-
-        checkOpenMM = run_subprocess("conda list openmm --json")
-        checkPdbfixer = run_subprocess("conda list pdbfixer --json")
-
-        if (checkOpenMM == "[]"):
+        try:
+            import openmm
+        except ModuleNotFoundError:
             raise ThirdPartyIntallationError(
-                "OpenMM is not installed in conda."
+                "OpenMM is not installed."
                 )
-        if (checkPdbfixer == "[]"):
+        try:
+            import pdbfixer
+        except ModuleNotFoundError:
             raise ThirdPartyIntallationError(
-                "OpenMM pdbfixer is not installed in conda."
+                "OpenMM pdbfixer is not installed."
                 )
         return None
 

src/haddock/modules/refinement/openmm/openmm.py

@@ -716,11 +716,17 @@ def run_openmm(
             qtemp = n * delta_temp
             integrator.setTemperature(qtemp * kelvin)
             simulation.step(int(eq_steps / nvt_sims))
+        # Try to obtain the degree of freedom
+        try:
+            dof = statereporter._dof
+        except AttributeError:
+            # may not exists if in implicit solvent..
+            dof = system.getNumParticles() * 3
         # Makes sure temperature of the system is reached
         self._stabilize_temperature(
             simulation,
-            qtemp,
-            statereporter._dof,
+            self.params["temperature_kelvin"],
+            dof,
             tolerance=5.0,
             steps=50
             )