[CP2K-user] [CP2K:19187] Transition state optimization with Dimer Method

[Alex Brown]

Dear Luca,

Thank you! Much appreciate. I will use your suggestions and come back here 
if I face any problems as I work on it. 

Thanks,
Alex


On Wednesday, 9 August 2023 at 05:05:08 UTC-4 luca bellucci wrote:

> Dear Axel,
> It is not necessary to evaluate and provide the dimer vectors, as the
> algorithm starts from a random distribution. Usually, after several
> steps, it is capable of identifying and pursuing a normal-mode with
> an imaginary frequency. If you want, you can extract the dimer-vectors
> from the atomic displacement of a specific normal mode. I do not have
> and I do not know if there exists such tool, but you can search it or
> do it on your own. In case, I can follow/help you in doing it.
> Anyway, to do it, you have to start from the definition of dimer vector
> and its relation with the normal mode displacements, see for example 
> https://doi.org/10.1063/1.480097
>
> However, this finding process is highly dependent on the initial
> conformation. Therefore, you must strive to discover the "correct
> conformation" or "distortion" most similar to the reaction path,
> attempting to eliminate erroneous vibrations (such as through
> minimization using a few steps of SD or CG). If, after several steps,
> the algorithm fails to identify the correct direction, you must alter
> the initial conformation. If needed, you can manually adjust the
> structure based on your intuition and propose a distortion along the
> reaction path.
> Regarding the input file, please try the following parameters:
> DR [angstrom] 0.001
> ANGLE_TOLERANCE [deg] 1.0
> INTERPOLATE_GRADIENT T
> At times, the following option might prove helpful:
> K-DIMER .TRUE.
> Probably, you have to increase the CUTOFF to 600 or higher value and
> try to use EXTRAPOLATION USE_GUESS.
>
> For more details it is necessary to have all the input data. 
>
> Cheers,
>
> Luca
>
> On Tue, 2023-08-08 at 17:54 -0700, Alex Brown wrote:
> > Dear Luca,
> > 
> > Thanks a lot for these suggestions. 
> > 
> > You mentioned that we need to evaluate and provide the vectors. How
> > does one evaluate it? Can you provide more insights on this?
> > 
> > Please find attached my input file. Let me know if anything looks
> > off.
> > 
> > Thanks,
> > Alex
> > 
> > On Tuesday, 8 August 2023 at 04:52:22 UTC-4 luca bellucci wrote:
> > > Dear Alex, 
> > > 
> > > By default, dimer vectors are assigned randomly. However, if you 
> > > prefer, you can assign each vector with its related keyword as
> > > follows: 
> > > DIMER/DIMER_VECTOR 
> > > 
> > > Currently, there are no tools available for ad-hoc generation, so
> > > you 
> > > need to evaluate and provide these vectors manually within the 
> > > DIMER_VECTOR section. Refer to a restart file for additional 
> > > information regarding the syntax. 
> > > 
> > > Your experience is quite common. Selecting a single configuration
> > > from 
> > > metadynamics does not guarantee convergence, also when the chosen 
> > > configuration closely resembles the transition state (TS). As a 
> > > practice, I typically extract 5-6 conformations from a molecular 
> > > dynamics (MD) simulation and perform a brief minimization using 
> > > conjugate gradient (CG), usually with no more than 4/5 steps
> > > depending 
> > > on the system. Subsequently, I initiate a dimer search on all
> > > these 
> > > configurations or choose the most promising ones. 
> > > 
> > > For more specific info, please provide the input file. 
> > > 
> > > Best regards, 
> > > 
> > > Luca 
> > > 
> > > 
> > > 
> > > On Mon, 2023-08-07 at 20:26 -0700, Alex Brown wrote: 
> > > > Dear CP2K Experts, 
> > > > 
> > > > I am trying to refine potential transition states I obtained
> > > from 
> > > > some Metadynamics calculations. I have looked at other
> > > conversations 
> > > > on here around implementing dimer method and have learned a
> > > little 
> > > > bit about that. 
> > > > 
> > > > I want to know how do one define the dimer vector for the 
> > > > calculation? I ran a calculation without specifying the dimer
> > > vector 
> > > > and the calculation fell into the reactant state. 
> > > > 
> > > > Does anyone have any tips for this? 
> > > > 
> > > > Also is there any drawback of my strategy of using Metadynamics 
> > > > calculation and guessing TS to later refine it? Just want to know
> > > if 
> > > > people would have some tips or suggestions on this idea. 
> > > > 
> > > > Thanks, 
> > > > Alex 
> > > > 
> > > > 
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