Add support for steered molecular dynamics with GROMACS. [ref #192]

python/BioSimSpace/Process/_gromacs.py

@@ -597,11 +597,6 @@ def _generate_config(self):
             # Convert the timestep to picoseconds.
             timestep = self._protocol.getTimeStep().picoseconds().magnitude()
 
-            # Get the metadynamics hill deposition frequency. We write GROMACS
-            # records at the same frequency so that the PLUMED data can be
-            # cross-referenced.
-            hill_freq = self._protocol.getHillFrequency()
-
             config.append("integrator = sd")                    # Leap-frog stochastic dynamics.
             config.append("ld-seed = %d" % seed)                # Random number seed.
             config.append("dt = %.3f" % timestep)               # Integration time step.
@@ -665,6 +660,92 @@ def _generate_config(self):
             setattr(self, "sampleConfigurations", self._sampleConfigurations)
             setattr(self, "getTime", self._getTime)
 
+        # Add configuration variables for a steered molecular dynamics protocol.
+        elif type(self._protocol) is _Protocol.Steering:
+
+            # Work out the number of integration steps.
+            steps = _math.ceil(self._protocol.getRunTime() / self._protocol.getTimeStep())
+
+            # Get the report and restart intervals.
+            report_interval = self._protocol.getReportInterval()
+            restart_interval = self._protocol.getRestartInterval()
+
+            # Cap the intervals at the total number of steps.
+            if report_interval > steps:
+                report_interval = steps
+            if restart_interval > steps:
+                restart_interval = steps
+
+            # Set the random number seed.
+            if self._is_seeded:
+                seed = self._seed
+            else:
+                seed = -1
+
+            # Convert the timestep to picoseconds.
+            timestep = self._protocol.getTimeStep().picoseconds().magnitude()
+
+            config.append("integrator = sd")                    # Leap-frog stochastic dynamics.
+            config.append("ld-seed = %d" % seed)                # Random number seed.
+            config.append("dt = %.3f" % timestep)               # Integration time step.
+            config.append("nsteps = %d" % steps)                # Number of integration steps.
+            config.append("nstlog = %d" % report_interval)      # Interval between writing to the log file.
+            config.append("nstenergy = %d" % report_interval)   # Interval between writing to the energy file.
+            config.append("nstxout = %d" % restart_interval)    # Interval between writing to the trajectory file.
+            if has_box and self._has_water:
+                config.append("pbc = xyz")                      # Simulate a fully periodic box.
+                config.append("cutoff-scheme = Verlet")         # Use Verlet pair lists.
+                config.append("ns-type = grid")                 # Use a grid to search for neighbours.
+                config.append("nstlist = 10")                   # Rebuild neigbour list every 10 steps.
+                config.append("rlist = 1.2")                    # Set short-range cutoff.
+                config.append("rvdw = 1.2")                     # Set van der Waals cutoff.
+                config.append("rcoulomb = 1.2")                 # Set Coulomb cutoff.
+                config.append("coulombtype = PME")              # Fast smooth Particle-Mesh Ewald.
+                config.append("DispCorr = EnerPres")            # Dispersion corrections for energy and pressure.
+            else:
+                config.append("pbc = no")                       # No boundary conditions.
+                config.append("cutoff-scheme = group")          # Generate pair lists for groups of atoms.
+                config.append("nstlist = 0")                    # Single neighbour list (all particles interact).
+                config.append("rlist = 0")                      # Zero short-range cutoff.
+                config.append("rvdw = 0")                       # Zero van der Waals cutoff.
+                config.append("rcoulomb = 0")                   # Zero Coulomb cutoff.
+                config.append("coulombtype = Cut-off")          # Plain cut-off.
+            config.append("vdwtype = Cut-off")                  # Twin-range van der Waals cut-off.
+            config.append("constraints = h-bonds")              # Rigid water molecules.
+            config.append("constraint-algorithm = LINCS")       # Linear constraint solver.
+
+            # Temperature control.
+            # No need for "berendsen" with integrator "sd".
+            config.append("tc-grps = system")               # A single temperature group for the entire system.
+            config.append("tau-t = 2.0")                    # 2ps time constant for temperature coupling.
+                                                            # Set the reference temperature.
+            config.append("ref-t = %.2f" % self._protocol.getTemperature().kelvin().magnitude())
+
+            # Pressure control.
+            if self._protocol.getPressure() is not None and has_box and self._has_water:
+                config.append("pcoupl = berendsen")         # Berendsen barostat.
+                config.append("tau-p = 1.0")                # 1ps time constant for pressure coupling.
+                config.append("ref-p = %.5f"                # Pressure in bar.
+                    % self._protocol.getPressure().bar().magnitude())
+                config.append("compressibility = 4.5e-5")   # Compressibility of water.
+
+            # Create the PLUMED input file and copy auxillary files to the working directory.
+            self._plumed = _Plumed(self._work_dir)
+            plumed_config, auxillary_files = self._plumed.createConfig(self._system, self._protocol)
+            self._setPlumedConfig(plumed_config)
+            if auxillary_files is not None:
+                for file in auxillary_files:
+                    file_name = _os.path.basename(file)
+                    _shutil.copyfile(file, self._work_dir + f"/{file_name}")
+            self._input_files.append(self._plumed_config_file)
+
+            # Expose the PLUMED specific member functions.
+            setattr(self, "getPlumedConfig", self._getPlumedConfig)
+            setattr(self, "getPlumedConfigFile", self._getPlumedConfigFile)
+            setattr(self, "setPlumedConfig", self._setPlumedConfig)
+            setattr(self, "getCollectiveVariable", self._getCollectiveVariable)
+            setattr(self, "getTime", self._getTime)
+
         # Set the configuration.
         self.setConfig(config)