have a working gmx wrapper that can run minimizations on single folda…

…mer systems, next is to build topologies for the entire system

.github/workflows/python-package.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v4

simulations/terphenyl_mop/tetramer_remd/t_250_450/bespoke/remd_parameters.yml

@@ -9,4 +9,4 @@ sim_id : sim
 build_foldamer : mop_tetramer.build
 param_method : bespoke
 n_replicas : 3
-gromacs_exe : 
+gromacs_exe : gmx

terphenyl_simulations/analysis_workflows/remd.py

@@ -103,11 +103,22 @@ def parameterize_foldamer(job):
         path = job.fn("")
     )
     top_generator.assign_parameters()
+    job.doc['foldamer_topology'] = top_generator.top_file
+    job.doc['foldamer_gro'] = top_generator.gro_file
 
 @FlowProject.pre.after(parameterize_foldamer)
 @FlowProject.operation
 def minimize_foldamer(job):
+    top_dir = os.path.abspath(".")
+    os.chdir(job.fn(""))
+    gmx_wrapper = terphenyl_simulations.gromacs_wrapper.GromacsWrapper(job.sp['gromacs_exe'])
+    out_name = job.doc['foldamer_gro'].split('.gro')[0] + '_centered.gro'
+    gmx_wrapper.center(job.doc['foldamer_gro'], out_name)
+    job.doc['foldamer_gro'] = out_name
+    gmx_wrapper.minimize(job.doc['foldamer_gro'], job.doc['foldamer_topology'])
 
+    os.chdir(top_dir)
+
 
 
 @FlowProject.pre.after(build_system)

terphenyl_simulations/build.py

@@ -234,8 +234,15 @@ def __init__(self, build_file_yml, ff_method, path="", ff_name = "openff-2.0.0")
                           'force field parameter generation methods. Please pick from:\n' + \
                             ' '.join(self._ff_generation_methods.keys()))
 
+        # Define other attributes populated by other functions
+        self.md_engine = None
+        self.top_file = None
+        self.gro_file = None
+
     def set_simulation_engine(self, md_engine_object):
         self.md_engine = md_engine_object
 
     def assign_parameters(self):
-        self.ff_generator.assign_parameters()
+        top_file, gro_file = self.ff_generator.assign_parameters()
+        self.top_file = top_file
+        self.gro_file = gro_file

terphenyl_simulations/force_fields.py

@@ -23,7 +23,8 @@ def __init__(self, mol_file, pdb_file, path="", ff_str="openff-2.0.0"):
 
     def assign_parameters(self, charge_method = 'am1bcc'):
         self._get_partial_charges(charge_method)
-        self._generate_ff_topologies()
+        top_file, gro_file = self._generate_ff_topologies()
+        return top_file, gro_file
 
     def _get_partial_charges(self, method="am1bcc"):
         sdf_file = os.path.join(
@@ -45,8 +46,12 @@ def _generate_ff_topologies(self):
         )
         interchange.positions = self.pdb_file.getPositions()
 
-        interchange.to_top(os.path.join(self.path, self.name + "_openff-2.0.0.top"))
-        interchange.to_gro(os.path.join(self.path, self.name + "_openff-2.0.0.gro"))
+        top_file = os.path.join(self.path, self.name + "_openff-2.0.0.top")
+        gro_file = os.path.join(self.path, self.name + "_openff-2.0.0.gro")
+        interchange.to_top(top_file)
+        interchange.to_gro(gro_file)
+
+        return top_file, gro_file
 
 
 

terphenyl_simulations/gromacs_wrapper.py

@@ -30,9 +30,16 @@ def __init__(self, gromacs_exe = None, path = '.'):
             self.mpi = True
             self.gmx = 'mpirun -np 1 ' + self.gmx
 
+    def center(self, gro_file, out_file):
+        editconf_call = self.gmx + ' editconf -f ' + gro_file + \
+                                            ' -c yes' + \
+                                            ' -o ' + out_file
+        process = subprocess.Popen(editconf_call.split(' '))
+        process.wait()
+
     def minimize(self, gro_file, top_file, prefix = 'em', mdp = 'em.mdp'):
         # Check for mdp file
-        if mdp not in os.listdir(self.path):
+        if not mdp in os.listdir(self.path):
             mdp = os.path.join(ROOT_DIR, 'data/simulation_templates/remd/em.mdp')
 
         # Run gmx grompp
@@ -50,7 +57,7 @@ def minimize(self, gro_file, top_file, prefix = 'em', mdp = 'em.mdp'):
         process = subprocess.Popen(mdrun_call.split(' '))
         process.wait()
 
-        
+