Something about MC project

Matt McGrath obfis... at gmail.com
Tue Mar 1 08:42:22 CET 2011


Hello Igor.  It seems to me that the problem is arising because you
have two molecules in the PSF file.  Due to some of the quirks of MC,
each molecule must be in its own PSF file (see some of the example
inputs in tests/MC/regtest to see how multiple molecules are dealt
with).  In addition, there should be only one molecule in the .psf
file even if there are multiple types of that molecule in the
simulation (NMOL tells CP2K to use the molecule specification in
the .psf file NMOL times).  The TOPOLOGY section should be something
like this:

    &TOPOLOGY
      CONNECTIVITY MOL_SET
      &MOL_SET
        &MOLECULE
          NMOL 1
          CONN_FILE_NAME topology_atoms_GLY.psf
        &END
        &MOLECULE
          NMOL 1
          CONN_FILE_NAME topology_atoms_H2O.psf
        &END
      &END
    &END

where the glycine molecule comes first in the COORD section, followed
by the water (if you have multiple molecules of water, they all come
after the glycine...if you have multiple glycine molecules, they all
come before the water).  This is so that MC knows which coordinates
belong to which molecule number (since MC moves choose a molecule type
at random, and then a molecule number at random, it cares much more
about molecules than MD).  The molecule name in the .psf file should
match the molecule name in the title of the psf file.  The psf file
will not change, no matter how many molecules of that type you have in
the simulation.

I hope this helps.

                                       Cheers, Matt

On Feb 28, 10:22 am, Igor Ying Zhang <wenx... at gmail.com> wrote:
> Dear all:
>
>      Recently, I want to use the Montecarlo module of CP2K to do some
> comformation analysis. At first time, I try a system only contains 1
> glycine and 1 water. However, the cp2k terminated abnormally without any
> error information. The attachment pleas find the input file and the
> corresponding psf file.
>
>      Any suggestions are wellcome :)
>
>      Best wishes!
>
> Igor Ying Zhang.
>
>  gly_h2o_1.psf
> 3KViewDownload
>
>  gly_h2o_1_mc.inp
> 2KViewDownload


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