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--- exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 19:39] – [Vibrational analysis] tmueller
+++ exercises:2016_uzh_cmest:path_optimization_neb [2016/10/31 08:23] – [Vibrational analysis] tmueller
@@ Line 227: / Line 227: @@
 To verify whether the point at the highest energy is actually a transition state, we will be doing a vibrational analysis.
-First identify the bead with the highest energy (see exercise above) and create a new XYZ file named ''ethane_neb_aba_TS.xyz'' with the respective coordinates (extracted from either the correct ''ethane_neb_aba-pos-Replica_nr_N-1.xyz'' file or the 'ethane_neb_aba_8r.xyz'').
+First identify the bead with the highest energy (see exercise above) and create a new XYZ file named ''ethane_neb_aba_TS.xyz'' with the respective coordinates (extracted from either the correct ''ethane_neb_aba-pos-Replica_nr_N-1.xyz'' file or the ''ethane_neb_aba_8r.xyz'').
-Use the following input file:
+Use the following input file and the same command as above (with different input and output file names of course) to generate the analysis.
 <code - ethane_TS_va.inp>
@@ Line 295: / Line 295: @@
         REPLICA_EVAL 1
       &END
-      &END
+    &END
   &END
 &END
 </code>
+Once this run completes, you should find a file ''ethane_TS_va-VIBRATIONS-1.mol''.
+Now we are going to use the application //molden// (which you can load using ''module load molden'') to visualize the vibrational modes:
+<code>
+$ molden ethane_TS_va-VIBRATIONS-1.mol
+</code>
+Click the //Norm. Mode// checkbox in the //Molden Control// window to list all the modes. What is the lowest frequency you get? By clicking on it you can visualize it.
+The presence of a  negative (imaginary) mode means that it is actually a transition state (and not stable).
+Now repeat the same steps presented here for the bead with the lowest energy. What is now the first frequency you get in the list? Is this geometry stable?
+Please note: while you should get only 18 different frequencies you get 21 instead. That means that 3 frequencies are global rotations instead of modes in the molecule and should be ignored when looking for negative frequencies to identify whether a conformer is stable or not.