Added an initial energies submit script for rsfe

cbc-univie · Aug 22, 2024 · 143d192 · 143d192
1 parent aac945b
commit 143d192
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diff --git a/transformato/bin/init_energies.sh b/transformato/bin/init_energies.sh
@@ -0,0 +1,14 @@
+path=$1
+
+cd ${path}
+pwd
+hostname
+
+
+istep=lig_in_vacuum
+python openmm_run.py -env vacuum -odcd ${istep}.dcd -sim False &> vacuum_init_energies_out.log
+
+# test
+
+istep=lig_in_waterbox
+python openmm_run.py -env waterbox -odcd ${istep}.dcd -sim False &> waterbox_init_energies_out.log
diff --git a/transformato/state.py b/transformato/state.py
@@ -488,6 +488,16 @@ def _copy_omm_files(self, intermediate_state_file_path: str):
             shutil.copyfile(
                 omm_simulation_submit_script_source, omm_simulation_submit_script_target
             )
+            omm_init_energies_submit_script_source = (
+                f"{self.configuration['bin_dir']}/init_energies.sh"
+            )
+            omm_init_energies_submit_script_target = (
+                f"{intermediate_state_file_path}/init_energies.sh"  
+            )
+            shutil.copyfile(
+                omm_init_energies_submit_script_source, omm_init_energies_submit_script_target
+            )
+
 
         elif self.configuration["simulation"]["free-energy-type"] == "rbfe":
             # parse omm simulation paramter