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Calculate vibrational frequencies with MOLCAS (Read 5531 times)
Gerrit-Jan Linker
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Calculate vibrational frequencies with MOLCAS
08.03.09 at 10:50:51
 
Calculate vibrational frequencies with MOLCAS
 
To calculate vibrational frequencies with MOLCAS you can to use the MCKINLY program.
 
Beware: Ensure you calculate the frequencies only when you are in a geometry minimum! The method used is only valid when the geometry is a minimum.
 
First compute the integrals using SEWARD
See: http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1202990912
 
Then either user SCF or RASSCF to calculate the wavefunctions
SCF: See http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1202990450
RASSCF: http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1211022024
 
After calculating the wavefunctions you can calculate the vibrational frequencies using the MCKINLEY program. The input for MCKINLEY to compute the vibrational frequencies is:
 

 &MCKINLEY &END
Perturbation
Hessian
End of input

 
Reference:
MCKINLEY description
http://www.teokem.lu.se/molcas/documentation/manual/node58.html
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« Last Edit: 09.03.09 at 14:06:06 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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MOLCAS vibrational analysis
Reply #1 - 08.03.09 at 17:19:30
 
MOLCAS vibrational analysis
 
In the molcas output file the frequencies and intensities of the vibrational modes are printed.
 
For analysis purposes it may be nice to use Molden and the molden output file. In my case the molden output file is called project.freq.molden.autosaved
 
Load it up with molden (use Read after staring molden or use molden project.freq.molden.autosaved as command line).
Tick the Norm. Mode box in the upper right corner of Molden's Molden Control palen to get the frequencies. A graph will be displayed with the vibrational spectum and a list of frequencies/intensities will be shown. Clicking on a peak in the plot will actually show the vibration in the main window of Molden by animating the structure.
 
See also:
Viewing Vibrations with Molden
http://www.cmbi.ru.nl/molden/vibration.html
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« Last Edit: 19.03.09 at 09:06:07 by Gerrit-Jan Linker »  

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Re: Calculate vibrational frequencies with MOLCAS
Reply #2 - 26.03.09 at 08:08:37
 
Mckinley/MCLR is memory hungry
 
The Mckinley/MCLR modules of Molcas are memory hungry. In a typical calculation in my project I can run with 1500 MB of memory. However Mckinley uses double that or even slightly more. In practise I am running now with 5000 MB and that is sufficient.
 
Therefore, before starting an expensive geometry optimalisation, ensure you allocate roughly double the amount of memory you need for the seward/scf steps in order for the job not to crash at the mckinley step.
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« Last Edit: 26.03.09 at 08:55:37 by Gerrit-Jan Linker »  

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Imaginary or Negative Frequencies
Reply #3 - 02.04.09 at 08:08:59
 
Imaginary or Negative Frequencies
 
Quote:
A stable structure should have no negative/imaginary frequencies. A transition state should have one negative/imaginary frequency. If your optimizer converged to a geometry with too many negative/imaginary frequencies, you will need to shift the geometry by hand, and re-run the optimization. Typically this happens with very floppy motions such as internal rotations and sometimes it can be difficult to avoid.

 
There are 3N cartesian degrees of freedom (N= the number of atoms in the molecule) and hence MCLR will output 3N frequencies.  
Edited:
There are 3 translational and 3 rotational degrees of freedom, these will have imaginary frequencies. 3N-6 normal modes remain. If the normal modes have no imaginary frequencies the geometry corresponds to a stationary point.

I don't think this is true. The following is:
 
There are 3 frequenties that are zero. These are due to translations. When they are not zero they should be very close to 0 (plus or minus). If not, the structure is not at its minimum.
In case there is a large negative frequency the geometry is optimised to a transition state. You are at a top of the Hessian and not in a minimum.
 
When optimising structures the vibrational frequencies can be calculated to ensure there are no saddle points. An indication of a saddle point is an imaginary frequency that does not correspond to a translation.
 
Sources:
Hints on Quantum Chemistry
http://ocw.mit.edu/NR/rdonlyres/Chemistry/5-68JSpring2003/309378CA-314C-4F31-AF2 E-DFA3C4993489/0/qchem.pdf
Geometry optimizations and Hessians
http://www.teokem.lu.se/molcas/tutor/node61.html
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« Last Edit: 23.05.12 at 19:59:04 by Gerrit-Jan Linker »  

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Publication about MOLCAS Mckinley
Reply #4 - 02.04.09 at 12:11:30
 
Publication about MOLCAS Mckinley
 
"A direct implementation of the second-order derivatives of multiconfigurational SCF energies and an analysis of the preconditioning in the associated response equation"
 
Author(s): Bernhardsson A, Lindh R, Olsen J, et al.
Source: MOLECULAR PHYSICS Volume: 96 Issue: 4 Pages: 617-628 Published: FEB 20 1999  
 
http://www.informaworld.com/smpp/content~content=a713830585~db=all
 
This article describes more the implementation than a description of the computed (vibrational and thermodynamic) properties.
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« Last Edit: 09.04.09 at 07:45:40 by Gerrit-Jan Linker »  

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Re: Calculate vibrational frequencies with MOLCAS
Reply #5 - 09.04.09 at 08:07:17
 
Thermodynamic properties calculated with MCLR
 
Quote:
...the zero-point energy correction and the thermal corrections to the total energy, internal, entropy, and Gibbs free energy. The analysis uses the standard expressions for an ideal gas in the canonical ensemble which can be found in any standard statistical mechanics book. The analysis is performed at different temperatures...

 
Example:
  Temperature  =  273.00  Kelvin  
  ---------------------------  
 
  DeltaG  =  59.90  kcal/mol  
  ZPVE  =  60.11  kcal/mol  
  TotDeltaU  =  60.72  kcal/mol  
  TotDeltaU  -  ZPVE  =  0.61  kcal/mol  
  DeltaS  =  3.0001  eu/mol  
  U(T&R)  =  1.6275  kcal/mol  
  Tot(temp)=  2.2393  kcal/mol  
 
Source:
Geometry optimizations and Hessians
http://www.teokem.lu.se/molcas/tutor/node61.html
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« Last Edit: 09.04.09 at 08:08:11 by Gerrit-Jan Linker »  

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