[CP2K-user] [CP2K:19874] Re: COLVAR for metaydnamics

[Tamal Das]

Hi,

    I have set up and run a metadynamics simulation using two bond
distances as the CV where the two bonds are forming during the reaction.
The calculation finished with my desired prediction. Now I am trying to
analyze the data and draw the free energy surface from the minimum energy
path. I am using the graph.psmp tool of CP2K for doing this. I have
generated the fes.dat file and mep.dat file. But I am facing some problems
to plot the FES. Could anyone help me to do the following things?

I want to draw the FES between energy and bond distance.
How can I extract the transition state structure from the free energy
surface? Calculate the free energy barrier etc.
How to get the bond distance which I have used as CV, from the
COLVAR.metadynLog file.

Please someone assist me regarding this problem.

best regards,
Tamal



On Fri, Feb 2, 2024 at 3:55 AM Marcella Iannuzzi <marci.akira at gmail.com>
wrote:

> Hi ..
>
> In the COLVAR description you can define POINT as POINT / TYPE GEO_CENTER
> of a list of POINT / ATOMS and use POINT / WEIGHTS if the atoms in the list
> have different masses and you want to use the COM
> Then depending on the specific COLVAR (for example the DISTANCE), the
> definition uses the list of POINTS
>
> Regards
> Marcella
>
> On Friday, February 2, 2024 at 8:46:09 AM UTC+1 bijayap... at gmail.com
> wrote:
>
>> Dear all,
>> I'm trying to carryout a metadynamics simulation using COM-COM distance
>> as my collective variable for a dimeric system.
>> I have done metadynamics simulations previously, but the CV was bond
>> distance.
>> Can anyone please help me with defining COM-COM distance as CV for
>> metadynamics ?
>> Thanking in advance.
>>
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