Frozen atoms in frequencies and transition states
Just Got Here
8:48:43 AM PDT - Mon, Jun 4th 2012
Hi,

i am new to NWchem and i am considering to use this software for one of my projects.

This project cosnitsts on a FROZEN-fragment attached to a non-FROZEN reactive species. Before switching to NWChem, I would need to know if the following is implemented in NWchem:

1. We need to be capable to run "local" frequncies for the non-Frozen part whicle the frozen atoms are present. I have attempted so with a water molecule and it doesn't seem to run. Should we use numerical frequencies or it is also implemented for analytical?

2. Also we would need to optimize transition states on the reactive species ( not frozen) attached to the Frozen fragment, would that be possible ?

Thanks,

nora

Forum Vet
10:46:16 AM PDT - Mon, Jun 4th 2012
On 2.: Yes, see http://nwchemgit.github.io/index.php/Release61:Geometry#Applying_constraints_in_geometry_opt... for details.

On 1. This may work in the numerical framework.

Thanks,

Bert


Quote:Noraplanas Jun 4th 3:48 pm
Hi,

i am new to NWchem and i am considering to use this software for one of my projects.

This project cosnitsts on a FROZEN-fragment attached to a non-FROZEN reactive species. Before switching to NWChem, I would need to know if the following is implemented in NWchem:

1. We need to be capable to run "local" frequncies for the non-Frozen part whicle the frozen atoms are present. I have attempted so with a water molecule and it doesn't seem to run. Should we use numerical frequencies or it is also implemented for analytical?

2. Also we would need to optimize transition states on the reactive species ( not frozen) attached to the Frozen fragment, would that be possible ?

Thanks,

nora

Just Got Here
1:25:02 PM PDT - Wed, Jun 6th 2012
Thanks for your answer.

Regarding point 2: My concern is if we are not able to calculate the frequencies in the numerical framework ( point 1) how is it possible to find the transition state without being sure we have the correct imaginary frequency.

Additionally, I haven't found infromation on how to run numrical frequencies in the manual... could somebody point me where to look?

Thanks!

Nora

Forum Vet
8:54:47 AM PDT - Thu, Jun 7th 2012
Point 2: With the geometry:actlist set ( http://nwchemgit.github.io/index.php/Release61:Geometry#Applying_constraints_in_geometry_opt... ), the geometry optimization will only take into account the gradients and hessian of the moving atoms. By default it will follow the first negative mode. See http://nwchemgit.github.io/index.php/Release61:Geometry_Optimization#Initial_Hessian and the section after that on how the initial mode is defined and found, and how you can modify if needed.

In general, if an analytic form of the gradient or hessian is not available, the code will do this automatically. Hence, no need to specify anything. But, for numerical: just add numerical to the end of the task line, i.e.

  task dft frequencies numerical

Thanks,

Bert



Quote:Noraplanas Jun 6th 8:25 pm
Thanks for your answer.

Regarding point 2: My concern is if we are not able to calculate the frequencies in the numerical framework ( point 1) how is it possible to find the transition state without being sure we have the correct imaginary frequency.

Additionally, I haven't found infromation on how to run numrical frequencies in the manual... could somebody point me where to look?

Thanks!

Nora


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