COLVAR for metaydnamics

[bijaya pathak]

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.

[Marcella Iannuzzi]

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

[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

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