[CP2K-user] Defining TOPOLOGY for GEMC simulations

[si...@umn.edu]

Hi, I am trying to do VLE simulations using *NVT*-GEMC simulations in CP2K. 
Right now I just have one molecule type. I am confused about the TOPOLOGY 
subsection. 

 

I have a system of 80 nitrogen molecules. I have three files, 
80_n2_coord.xyz (contains the coordinates of 80 N2 molecules i.e. 160 N), 
80_n2_connectivity.psf (connectivity file for 80 N2 molecules), and 
1_n2_connectivity.psf (connectivity file for 1 N2 molecule).

 

When I use the 80 molecule connectivity file (using following commands) : 

    &COORD

      @INCLUDE 80_n2_coord.xyz

    &END COORD

   &TOPOLOGY

      CONN_FILE_FORMAT               PSF

      CONN_FILE_NAME                   80_n2_connectivity.psf

    &END TOPOLOGY

It gives me an error:

Did not find MOLECULE sections for every molecule in the simulation 

 (make sure both input files have all types)

This TOPOLOGY section worked fine for me when I did FIST  (Force field 
-based) MD simulations of the same system.

 

 

And when I use the 1 molecule connectivity file (using following commands) :

    &COORD

      @INCLUDE 80_n2_coord.xyz

    &END COORD

   &TOPOLOGY

      CONN_FILE_FORMAT       MOL_SET

      &MOL_SET

        &MOLECULE

          CONN_FILE_NAME       nitrogen_bias.psf

          NMOL       80

        &END MOLECULE

      &END MOL_SET

    &END TOPOLOGY

It runs fine.  

Also, if I use 80_n2_connectivity.psf in &MOLECULE, it gives the same 
error. 

 

I have following questions regarding this situation:

 

i) Why CP2K does not accept the 80 molecule psf file directly for MC 
simulations? Why do I need to define the &MOLECULE section for each 
molecule type? And why does MD simulations run fine without &MOLECULE 
section.

 

 

ii)  How does CP2K create the whole system from the PSF file of just one 
molecule? How does it figure out the bonds between 160 atoms just from the 
PSF file of one molecule?

 

iii) Is there a way to avoid defining &MOLECULE section and providing the 
connectivity of the whole system using just one .psf file?

 


Thanks,

Ramanish

 
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