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--- exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 19:28] – [Visualize the trajectory] tmueller
+++ exercises:2016_uzh_cmest:path_optimization_neb [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 222: / Line 222: @@
 Create a plot for this energy curve.
+====== Vibrational analysis ======
+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'').
+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>
+&GLOBAL
+  PROJECT ethane_TS_va
+  RUN_TYPE NORMAL_MODES
+  PRINT_LEVEL MEDIUM
+&END GLOBAL
+&FORCE_EVAL
+  METHOD Quickstep              ! Electronic structure method (DFT,...)
+  &DFT
+    BASIS_SET_FILE_NAME  BASIS_MOLOPT
+    POTENTIAL_FILE_NAME  POTENTIAL
+    &POISSON                    ! Solver requested for non periodic calculations
+      PERIODIC XYZ
+    &END POISSON
+    &SCF                        ! Parameters controlling the convergence of the scf. This section should not be changed.
+      SCF_GUESS ATOMIC
+      EPS_SCF 1.0E-7
+      MAX_SCF 300
+    &END SCF
+    &XC                        ! Parametes needed to compute the electronic exchange potential
+      &XC_FUNCTIONAL PBE
+      &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 12. 12. 12.
+      PERIODIC XYZ
+    &END CELL
+    &TOPOLOGY                    ! Section used to center the atomic coordinates in the given box. Useful for big molecules
+      &CENTER_COORDINATES
+      &END
+      COORD_FILE_FORMAT xyz
+      COORD_FILE_NAME  ./ethane_neb_aba_TS.xyz
+    &END
+    &KIND H
+      ELEMENT H
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q1
+    &END KIND
+    &KIND C
+      ELEMENT C
+      BASIS_SET DZVP-MOLOPT-GTH
+      POTENTIAL GTH-PBE-q4
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+&VIBRATIONAL_ANALYSIS
+  NPROC_REP 1
+  DX 0.01
+  FULLY_PERIODIC
+  &PRINT
+    &MOLDEN_VIB
+    &END
+    &CARTESIAN_EIGS
+    &END
+    &PROGRAM_RUN_INFO
+      &EACH
+        REPLICA_EVAL 1
+      &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.