Plumed Driver error message "Error converting i"

[jerryt...@gmail.com]

Hi,
I'm relatively new to plumed and was trying to use plumed driver to post-process my metadynamics run.  When using the command line:

plumed driver --plumed plumed.dat --ixyz Nitros_to_DMA-pos-1.xyz --trajectory-stride 1 --timestep 0.001 --kt 2.49

I get 'Error converting i' message.  I have attached my plumed.dat and the full driver output (PLUMED.out).

Any help you can provide would be greatly appreciated.
Thank you,

Jerry

[jerryt...@gmail.com]

I think I've found the cause of the error, but I'm not sure how to fix it:

I'm using plumed with CP2K, printing out every trajectory to Nitros_to_DMA-pos-1.xyz.  Output to the xyz file for each MD step begins with:

     668
 i =        0, time =        0.000, E =     -3842.2078052158
  O        -0.4923300000        4.3934600000        2.3056700000
  O         1.7437100000        0.2195500000       -0.9749000000
  N         0.3609100000        4.1370200000        1.5522100000
...

It seems the output format is confusing plumed??

Thanks again,

Jerry

[Omar Valsson]

Hello Jerry, 

I think that the --ixyz format requires information about the box dimensions in the second line of each coordinate entry in the xyz file. You can specify the box dimensions with the --box flag in the plumed driver, and I think it will then not read the box dimensions from the xyz file. However, this will only work correctly if you are performing NVT simulations and the box dimensions are fixed; in NPT, distances and other CVs that use the nearest-image convention for calculation will not work correctly if you use the --box flag. Also, you need to be careful to use the right box dimensions and units passed to the --box flag as that will be used in distance calculations. You should do some tests to make sure that you are getting sensible values from your CV calculations. 

This is what plumed driver -h says about the --box flag:

                  --box - comma-separated box dimensions (3 for orthorhombic, 9 for
                          generic)

Best regards,

Omar 

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[jerryt...@gmail.com]

Hi Omar,

Thank you.  It was the xyz format.  I included the --box flag and everything worked out.

Thanks again,

Jerry