add warning, fix tutorial

the random flag of convert shouldnt be used with gaussian linker domains
added a warning (just a print message) removed this flag from the
tutorial...

pycomplexes/pycomplexes/convert.py

@@ -258,9 +258,12 @@ def __init__(self, node, name, randomize=False, box=None):
 
         # guess connections for gaussian domains
         guessed_connections = []
+        flag_linkers_plus_random_placement=False
         for dom in self.domains:
             n = dom.node
             if dom.type == "gaussian":
+                if randomize:
+                    flag_linkers_plus_random_placement=True
                 start_atom = u.select_atoms(n["start_connection"][1])
                 if start_atom.n_atoms != 1:
                     raise RuntimeError(
@@ -287,7 +290,11 @@ def __init__(self, node, name, randomize=False, box=None):
                 }
                 guessed_connections.append(con3)
                 dom._metadata['connection_id'] = len(guessed_connections) - 1
-
+        if flag_linkers_plus_random_placement:
+            print("WARNING: You used the randomized starting position in combination with Gaussian linker domains!")
+            print("The random placement does not respect the distance restraints, " +
+                  "which are implied by the Gaussian linker domains")
+            print("We strongly recommend not to combine random initial placement with Gaussian Linker domains!")
 
         # update connections
         connections = node.get("connections", dict())
@@ -477,7 +484,7 @@ def parser(p):
         p.add_argument("--debye_length", type=float, default=10)
         p.add_argument("--dielectric_constant", type=float, default=80)
         p.add_argument(
-            "--random", type=bool, help="random placement of the topologies in the box"
+            "--random", action="store_true", help="random placement of the topologies in the box"
         )
         p.add_argument(
             "--list_forcefields",

tutorials/Linker/chmp3_simulations.ipynb

@@ -20,7 +20,7 @@
    "outputs": [],
    "source": [
     "%%writefile chmp3.top\n",
-    "box: [100, 100, 100]\n",
+    "box: [200, 200, 200]\n",
     "topology:\n",
     "    CHMP3:\n",
     "        coordinate-file: chmp3.pdb\n",
@@ -59,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pycomplexes convert chmp3.top chmp3.cplx --random=True"
+    "!pycomplexes convert chmp3.top chmp3.cplx"
    ]
   },
   {
@@ -126,15 +126,6 @@
     "!pycomplexes visualize -cc config.yaml"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pwd"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},