Montecarlo

Francesco francesc... at gmail.com
Tue Nov 9 16:09:11 CET 2010


Hi Matt,

Thanks for your psf file, but I cannot obtain the conformational
analysis for a single ethane molecule, with any attempts I have done.

After 1000 steps I obtain just small volume changes, that of course,
for a single molecule is not useful.
If I block the volume variations, in the output file ethane.inp.moves
I obtain just empty_avbmc movements, i.e. the program does nothing.

I started to look in the literature for some information about AVBMC
method: is it suitable for conformational analysis also for single
molecules? Every application I found is about condensed phase.

Could you paste the whole input file? I guess I cannot understand how
to use some keyword.

Thank you in advance,
Francesco

On Sep 15, 9:53 am, Matt <obfis... at gmail.com> wrote:
> Hello Francesco.
>
> One of the quirks with MC in CP2K is that it needs topology files
> defined for every molecule type.  The reason is because we noticed
> that the code would crash sometimes during a regular NVT run when CP2K
> found that the number of molecules had changed (the automatic
> molecular determination).
>
> I have everything working with the following .psf file and topology
> section:
>
>     &TOPOLOGY
>       CONNECTIVITY MOL_SET
>       &MOL_SET
>         &MOLECULE
>           NMOL 1
>           CONN_FILE_NAME topology_atoms_ETH.psf
>         &END
>       &END
>     &END
>
> Make sure that the coordinates in the input file match the order in
> the topology file (i.e. hydrogens 3,4,5 are bonded to carbon 1).  This
> is a rather clumsy way to do it, but it's the best I could come up
> with when designing the routines.  The most difficult part of this is
> creating the psf file: the formatting is VERY strict (number of
> spaces), and a slight mistake will cause a seg fault (as I discovered
> when creating this file).  I took the format from cp2k/tests/Fist/
> sample_psf/solute1.psf.  Good luck!
>
>                                   Cheers, Matt
>
>  PSF EXT
>
>          1 !NTITLE
>      Topology file for ethane
>
>          8 !NATOM
>          1 ETH             1 ETH      C       C       0.000000
> 12.000000        0
>          2 ETH             1 ETH      C       C       0.000000
> 12.000000        0
>          3 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>          4 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>          5 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>          6 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>          7 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>          8 ETH             1 ETH      H       H       0.000000
> 1.008000        0
>
>          7 !NBOND
>          1         2         1         3         1         4
> 1         5
>          2         6         2         7         2         8
>
>          6 !NTHETA
>          3         1         2         4         1         2
> 5         1         2
>          6         2         1         7         2         1
> 8         2         1
>
>          9 !NPHI
>          3         1         2         6         4         1
> 2         6
>          5         1         2         6         3         1
> 2         7
>          4         1         2         7         5         1
> 2         7
>          3         1         2         8         4         1
> 2         8
>          5         1         2         8
>
>          0 !NIMPHI
>
>          0 !NDON
>
>          0 !NACC
>
>          0 !NNB
>
>          0 !NGRP
>
> On Sep 14, 7:38 pm, Francesco <francesc... at gmail.com> wrote:
>
>
>
>
>
>
>
> > Hi to all,
>
> > I would like to use the CP2K-Montecarlomodule in order to do a
> > conformational analysis test, with DFT.
>
> > In order to understand what to do, I have started with ethane (and
> > other small molecules), but any attempt failed till now. I've used the
> > file in the regtest as a template, but in the best case I obtained the
> > error attached below.
>
> > After some tests, it seems to me that the Number of molecule types
> > vary as the number of atoms: I tried also to define a psf file, but
> > with other errors. By the way with "CONN_FILE_FORMAT OFF" should
> > overcome this request. Or am I wrong?
>
> > Has anybody of you done something similar?
> > Any help will be appreciated.
>
> > Thanks in advance,
> > Francesco
>
> > --------------------------------------------------------------------------- -----
> >  Number of molecule types            8
> >  &MOLECULE sections found            1
>
> >  *
> >  *** ERROR in mc_types.F/mc_input_file_create  ***
> >  *
>
> >  *** Did not find MOLECULE sections for every molecule in the
> > simulation  ***
> >  *** (make sure both input files have all
> > types)                          ***
>
> > --------------------------------------------------------------------------- -------
> > &FORCE_EVAL
> >   METHOD Quickstep
> >   &DFT
> >     &MGRID
> >       CUTOFF 100
> >     &END MGRID
> >     &QS
> >       EXTRAPOLATION USE_PREV_WF
> >     &END QS
> >     &SCF
> >       SCF_GUESS ATOMIC
> >     &END SCF
> >     &XC
> >       &XC_FUNCTIONAL Pade
> >       &END XC_FUNCTIONAL
> >       &XC_GRID
> >         XC_DERIV SPLINE2
> >         XC_SMOOTH_RHO NONE
> >       &END XC_GRID
> >     &END XC
> >   &END DFT
> >   &SUBSYS
> >     &CELL
> >       ABC 5.04977 5.04977 5.04977
> >     &END CELL
> >     &COORD
> >  C     0.000000     0.000000     0.000000
> >  C     0.000000     0.000000     1.450000
> >  H     1.026720     0.000000     1.812996
> >  H    -0.513360     0.889165     1.813000
> >  H    -0.513360    -0.889165     1.813000
> >  H    -1.026719     0.000000    -0.363000
> >  H     0.513360     0.889165    -0.363000
> >  H     0.513360    -0.889165    -0.363000
> >     &END COORD
> >     &KIND H
> >       BASIS_SET DZVP-GTH-Pade
> >       POTENTIAL GTH-BLYP-q1
> >     &END KIND
> >     &KIND C
> >       BASIS_SET DZVP-GTH-Pade
> >       POTENTIAL GTH-BLYP-q4
> >     &END KIND
> >     &TOPOLOGY
> >       &MOL_SET
> >         &MOLECULE
> >           NMOL 1
> >           CONN_FILE_FORMAT OFF
> >         &END MOLECULE
> >       &END MOL_SET
> >       CONNECTIVITY MOL_SET
> >     &END TOPOLOGY
> >   &END SUBSYS
> > &END FORCE_EVAL
> > &GLOBAL
> >   PROJECT ethane_MC
> >   RUN_TYPE MC
> >   PRINT_LEVEL LOW
> > &END GLOBAL
> > &MOTION
> >   &MC
> >     IUPTRANS 6400000
> >     IUPVOLUME 3200000
> >     LBIAS no
> >     LSTOP yes
> >     NMOVES 8
> >     NSTEP 2
> >     PMSWAP 0.0
> >     PMTRAION 0.00
> >     PMTRANS 0.00
> >     PMVOLUME 1.00
> >     PMVOL_BOX 1.00
> >     PRESSURE 1.013
> >     ENSEMBLE traditional
> >     RESTART no
> >     RESTART_FILE_NAME mc_restart_1
> >     RMDIHEDRAL 3.0
> >     RMANGLE 3.0
> >     RMBOND 0.074
> >     RMROT 26.0
> >     RMTRANS 0.38
> >     RMVOLUME 0.5
> >     TEMPERATURE 398.0
> >     AVBMC_RMIN 1.0
> >     AVBMC_RMAX 5.0
> >     AVBMC_ATOM 1
> >     PBIAS 0.5
> >     ETA 0.0
> >     PMAVBMC_MOL 1.0
> >     PMSWAP_MOL 1.0
> >     PMROT_MOL 1.0
> >     PMTRANS_MOL 1.0
> >     PMTRAION_MOL 1.0
> >     VIRIAL_TEMPS 300.0
> >   &END MC
> > &END MOTION


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