add vacuum minimization step to the MD workflows

cwl_adapters/combine_structure.cwl

@@ -12,7 +12,7 @@ baseCommand: ['python', '/combine_structure.py']
 
 hints:
   DockerRequirement:
-    dockerPull: ndonyapour/combine_structure
+    dockerPull: ndonyapour/combine_structure_zip
 
 inputs:
   input_structure1:
@@ -40,6 +40,20 @@ inputs:
     - edam:format_3877 
     inputBinding:
       prefix: --input_structure2
+
+  input_top_zip_path:
+    label: Input zip file
+    doc: |-
+      Input zip file
+      Type: string
+      File type: input
+      Accepted formats: zip
+      Example file: https://github.com/bioexcel/biobb_md/blob/master/biobb_md/test/data/gromacs/genion.zip
+    type: File
+    format:
+    - edam:format_3987
+    inputBinding:
+      prefix: --input_top_zip_path
 
   output_structure_path:
     label: Output combined PDB file path

examples/config_ci.json

@@ -10,7 +10,11 @@
         "vs_demo_2_weekly",
         "vs_demo_3_weekly",
         "vs_demo_4_weekly",
-        "docking_rescoring_weekly"
+        "docking_rescoring_weekly",
+        "stability",
+        "docking_stability",
+        "nmr",
+        "tutorial"
     ],
     // NOTE: Most of the workflows in this list have free variables because they are subworkflows
     // i.e. if you try to run them, you will get "Missing required input parameter"

examples/docking/docking.wic

@@ -98,8 +98,9 @@ steps:
       - output_top_zip_path: !& complex_vac.zip
     combine_structure:
       in:
-        input_structure1: !* receptor.xyz  # receptor_hydrogens.pdb
+        input_structure1: !* receptor.xyz #  !* receptor_hydrogens.pdb
         input_structure2: !* pose_ligand.xyz
+        input_top_zip_path: !* complex_vac.zip
       out:
       - output_structure_path: !& complex_vac.pdb
 

examples/docking/docking_stability.wic

@@ -20,6 +20,7 @@ steps:
       dt: !ii 0.002
       temperature: !ii 298.0
       pressure: !ii 1.0
+
 wic:
   graphviz:
     label: Docking + MD Stability Analysis
@@ -31,12 +32,31 @@ wic:
       wic:
         inlineable: False
         steps:
+          (1, setup_vac_min.wic):
+            wic:
+              steps:
+                (3, solv_ion.wic):
+                  wic:
+                    steps:
+                      (4, genion):
+                        out:
+                        - output_top_zip_path: !& genion_complex.zip
           (2, basic.wic):
+            in:
+              top_zip_path: !* genion_complex.zip
             wic:
               steps:
                 (3, prod.wic):
                   wic:
                     steps:
+                      (2, grompp):
+                        in:
+                          input_top_zip_path: !* genion_complex.zip
+                      (3, mdrun):
+                        out:
+                        - output_crd_path: !& prod_complex.gro  # overload prod.gro
+                        - output_trr_path: !& prod.trr
+                        - output_edr_path: !& prod.edr
                       (4, cwl_subinterpreter_analysis.wic):
                         wic:
                           implementation: complex
@@ -45,4 +65,8 @@ wic:
               steps:
                 (1, analysis_realtime.wic):
                   wic:
-                    implementation: complex
+                    implementation: complex
+                (2, analysis_final.wic):
+                  wic:
+                    implementation: complex
+

examples/docking/gen_topol_params.wic

@@ -78,6 +78,7 @@ steps:
     in:
       input_structure1: input_receptor_xyz_path
       input_structure2: !* pose_ligand.xyz
+      input_top_zip_path: !* complex_vac.zip
     out:
     - output_structure_path: !& complex_vac.pdb
 

examples/docking/vs_demo_2.wic

@@ -155,14 +155,19 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.wic):
+          (1, setup_vac_min.wic):
             wic:
               steps:
-                (4, genion):
-                  out:
-                  - output_top_zip_path: !& genion_complex.zip
+                (3, solv_ion.wic):
+                  wic:
+                    steps:
+                      (4, genion):
+                        out:
+                        - output_top_zip_path: !& genion_complex.zip
           (2, basic.wic):
-            wic:
+            in: 
+              top_zip_path: !* genion_complex.zip
+            wic: 
               steps:
                 (3, prod.wic):
                   wic:

examples/docking/vs_demo_3.wic

@@ -127,18 +127,24 @@ wic:
     (7, gen_topol_params.wic):
       wic:
         inlineable: False
+
     (8, stability.wic):
       wic:
         inlineable: False
         steps:
-          (1, setup.wic):
+          (1, setup_vac_min.wic):
             wic:
               steps:
-                (4, genion):
-                  out:
-                  - output_top_zip_path: !& genion_complex.zip
+                (3, solv_ion.wic):
+                  wic:
+                    steps:
+                      (4, genion):
+                        out:
+                        - output_top_zip_path: !& genion_complex.zip
           (2, basic.wic):
-            wic:
+            in: 
+              top_zip_path: !* genion_complex.zip
+            wic: 
               steps:
                 (3, prod.wic):
                   wic:

examples/docking/vs_demo_4.wic

@@ -206,14 +206,19 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.wic):
+          (1, setup_vac_min.wic):
             wic:
               steps:
-                (4, genion):
-                  out:
-                  - output_top_zip_path: !& genion_complex.zip
+                (3, solv_ion.wic):
+                  wic:
+                    steps:
+                      (4, genion):
+                        out:
+                        - output_top_zip_path: !& genion_complex.zip
           (2, basic.wic):
-            wic:
+            in: 
+              top_zip_path: !* genion_complex.zip
+            wic: 
               steps:
                 (3, prod.wic):
                   wic:

examples/gromacs/basic.wic

@@ -1,4 +1,8 @@
 inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
   nsteps:
     type: int
   dt:
@@ -15,14 +19,16 @@ steps:
 # (i.e. immediately before molecular dynamics) so we can extract &min.tpr
 # to this level and use the following syntax to pass it to only one call site.
 # (Moreover, the former will create multiple definitions of &min.tpr, which is not allowed.)
-    min.wic:
-    equil.wic:
-    prod.wic:
-      in:
-        nsteps: nsteps
-        dt: dt
-        ref-t: ref-t
-        ref-p: ref-p
+  min.wic:
+    in:
+      top_zip_path: top_zip_path
+  equil.wic:
+  prod.wic:
+    in:
+      nsteps: nsteps
+      dt: dt
+      ref-t: ref-t
+      ref-p: ref-p
 
 # Pass the CWL `in` tag as a parameter through BOTH of the yml DSL tags cg.wic and grompp.
 # Use (1-based) indexing to uniquely reference (step_number, step_name).

examples/gromacs/cg.wic

@@ -1,32 +1,39 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
-    grompp:
-      in:
-        config: !ii
-          mdp:
-            integrator: cg
-            define: -DFLEXIBLE # Defines a flexible water model if it exists in the system
-            # https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html#conjugate-gradient
-            rvdw: 1.4
-            rcoulomb: 1.4
-            #coulombtype: PME
-            nsteps: 1000
-            emstep: 0.01
-            emtol: 10
-            nstxout: 100
-            nstenergy: 1
-    mdrun:
-      in:
-        nb_terms: !ii cpu  # NOTE: Workaround for a bug in gromacs 2022.2, fixed in 2022.3
-        # https://manual.gromacs.org/current/release-notes/2022/2022.3.html#energy-minimization-would-not-converge-with-gpu-and-without-dd
-        bonded_terms: !ii cpu # GPU implementation IS supported for md integrator, is NOT supported for sd integrator, etc.
-        pme_terms: !ii cpu
-        pme_fft_terms: !ii cpu
-        update_terms: !ii cpu
-    gmx_energy:
-      in:
-        config: !ii
-          terms: [Potential]
-        output_xvg_path: !ii energy_min_cg.xvg
+  grompp:
+    in:
+      input_top_zip_path: top_zip_path
+      config: !ii
+        mdp:
+          integrator: cg
+          define: -DFLEXIBLE # Defines a flexible water model if it exists in the system
+          # https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html#conjugate-gradient
+          rvdw: 1.4
+          rcoulomb: 1.4
+          #coulombtype: PME
+          nsteps: 1000
+          emstep: 0.01
+          emtol: 10
+          nstxout: 100
+          nstenergy: 1
+  mdrun:
+    in:
+      nb_terms: !ii cpu  # NOTE: Workaround for a bug in gromacs 2022.2, fixed in 2022.3
+      # https://manual.gromacs.org/current/release-notes/2022/2022.3.html#energy-minimization-would-not-converge-with-gpu-and-without-dd
+      bonded_terms: !ii cpu # GPU implementation IS supported for md integrator, is NOT supported for sd integrator, etc.
+      pme_terms: !ii cpu
+      pme_fft_terms: !ii cpu
+      update_terms: !ii cpu
+  gmx_energy:
+    in:
+      config: !ii
+        terms: [Potential]
+      output_xvg_path: !ii energy_min_cg.xvg
 
 wic:
   graphviz:

examples/gromacs/equil.wic

@@ -1,6 +1,6 @@
 steps:
-    nvt.wic:
-    npt.wic:
+  nvt.wic:
+  npt.wic:
 
 wic:
   graphviz:

examples/gromacs/min.wic

@@ -1,9 +1,19 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
-    steep.wic:
+  steep.wic:
+    in:
+      top_zip_path: top_zip_path
 # Fatal error:
 # The coordinates could not be constrained. Minimizer 'cg' can not handle
 # constraint failures, use minimizer 'steep' before using 'cg'.
-    cg.wic:
+  cg.wic:
+    in:
+      top_zip_path: top_zip_path
 # Fatal error:
 # The combination of constraints and L-BFGS minimization is not implemented.
 # Either do not use constraints, or use another minimizer (e.g. steepest