Changes between Initial Version and Version 1 of AlkaneCreation

Timestamp:

Jun 16, 2011, 4:37:24 PM (14 years ago)

Author:

FrederikHeber

Comment:

first version

AlkaneCreation

@@ +1 @@
+=== Creating Arbitrary Alkanes ===
+
+This can also be used (in a somewhat unusual way) to generate alkanes of arbitrary length from a given one. Assume, we have a propane as given. We cut off the terminal hydrogens at either end and place them in files ''buildingblock_upper.xyz'' 
+{{{
+./molecuilder -i buildingblock_upper.xyz --select-all-atoms -t "-8.3885,-1.5127,-0.89"
+}}}
+where we translate the position such that its carbon bond partner would be at "0,5,5".
+
+In the same way we proceed with the hydrogen at the other end stored in ''buildingblock_lower.xyz''. 
+{{{
+./molecuilder -i buildingblock_lower.xyz --select-all-atoms -t "-12.1362,-0.6293,-0.89"
+}}}
+where we again translate the position such that its carbon bond partner would be at "0,5,5".
+
+Furthermore, we cut out the first pair of carbon atoms along with the four hydrogens (not the terminal one) and store it in ''buildingblock_center.xyz''. Then we may proceed as follows to produce a decane.
+{{{
+./molecuilder -i decane.xyz --change-box "2.4985,0,10,0,0,10" -l buildingblock_center.xyz --repeat-box "5,1,1"
+}}}
+where we obtained the box length from the distance of one carbon atom to its next-nearest neighbor.
+
+That is:
+ * first, we use ''-i'' to store everything in a new file ''decane.xyz''.
+ * Next, we set the box dimensions (''--change-box'') to fit with the periodicity of the alkanes, here in the x direction.
+ * Then, we load (''-l'') the atoms into this domain.
+ * Finally, we call ''--repeat-box'' the create five copies from the given segment containing two carbons.
+
+At last, we need to re-attach the terminal hydrogen atoms. First the lower part, which is easier
+{{{
+./molecuilder -i decane.xyz -l buildingblock_lower.xyz
+}}}
+Then the upper part which has to be translated to its destination
+{{{
+./molecuilder -i decane.xyz -l buildingblock_upper.xyz --select-molecule-by-order -1 --select-molecules-atoms -t "11.24325,0,0"
+}}}
+where the translation factor is 4.5 times the above periodicity in the x direction.
+
+And finally, we have a complete decane molecule.
+
+Now, one may ask: Why not do this in a text editor? Of course, the duplication along with the translation of the periodic section is nice. Moreover this approach can easily be placed in a script and arbitrary alkanes can be produced.