Montecarlo
Francesco
francesc... at gmail.com
Tue Nov 9 15:09:11 UTC 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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