[CP2K:4969] SE MD in CP2K
Bharat Sharma
bharats... at gmail.com
Wed Feb 19 17:11:30 UTC 2014
Hello Jeurg,
Thank you for your reply. If it is special case for SCP-NDDO (PNNL), how
about for PM3 and PM6 methods? (Paper includes PM3, PM6 and SCP-NDDO
methods) I performed SE-MD calculation (NVT) with PM3 using whatever the
controls mentions in the paper, but O-H bond lengths increases too much
(more than 3 angstrom). I think I am missing something in the input file.
I will use PNNL method also and see what happens.
Thank you.
Bharat Sharma
On Wed, Feb 19, 2014 at 11:53 AM, <hut... at chem.uzh.ch> wrote:
> Hi
>
> that paper uses a special NDDO version adapted for periodic systems.
> To do such a calculation you need a section like this
>
> &DFT
> &QS
> METHOD PNNL
> &SE
> SCP T
> INTEGRAL_SCREENING SLATER
> &END
> &END QS
> &SCF
> &OUTER_SCF
> # TYPE SCP
> EPS_SCF 1.0E-8
> MAX_SCF 20
> &END OUTER_SCF
> SCF_GUESS ATOMIC
> EPS_SCF 1.0E-8
> MAX_SCF 20
> &OT T
> MINIMIZER DIIS
> SCP_NDDO T
> PRECONDITIONER FULL_ALL
> &END OT
> &END SCF
> &END DFT
>
> regards
>
> Juerg Hutter
>
> --------------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Institut für Chemie FAX : ++41 44 635 6838
> Universität Zürich E-mail: hut... at chem.uzh.ch
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com wrote: -----
> To: cp... at googlegroups.com
> From: bharat
> Sent by: cp... at googlegroups.com
> Date: 02/18/2014 09:07PM
> Subject: [CP2K:4957] SE MD in CP2K
>
> Hello Everyone,
>
> I am trying to reproduce the results published on J. Phy. Chem. A by G.
> Murdachaew et al. (http://pubs.acs.org/doi/abs/10.1021/jp110481m). I used
> the similar control parameters described in the paper. The simulation is
> for 64 water molecules. After 30 steps, structure is terribly going wrong.
> O-H distance increases too much (>3Angstrom).
>
> The initial coordinates are used from
> http://pubs.acs.org/doi/abs/10.1021/jz401931f.
> Please find input file, output file, and dcd file here.
> https://drive.google.com/folderview?id=0B56PcAs22G9NdEd4eWh3ekFTd3c&usp=sharing
>
>
> Can anyone help me to figure out where I am doing wrong?
>
>
> Thank you.
>
> Bharat
>
> @SET CURR_I 01
>
> #@SET SEED 1000
> &EXT_RESTART
> RESTART_FILE_NAME ./wt_bk_AM101-1.restart
> &END EXT_RESTART
> &GLOBAL
> PROGRAM_NAME CP2K
> PROJECT_NAME wt_bk_AM1${CURR_I}
> RUN_TYPE MD
> # SEED ${SEED}
> PREFERRED_FFT_LIBRARY FFTW
> # ECHO_INPUT YES
> PRINT_LEVEL LOW
> SAVE_MEM
> &END GLOBAL
>
> &MOTION
> # &PRINT
> # &FORCES
> # FORMAT XMOL
> # &END FORCES
> # &END PRINT
> &MD
> ENSEMBLE NVT
> STEPS 10000
> TIMESTEP 0.50
> TEMPERATURE 300
> &THERMOSTAT
> TYPE NOSE
> REGION MASSIVE
> &NOSE
> LENGTH 3
> YOSHIDA 3
> TIMECON 100
> MTS 2
> &END NOSE
> &END THERMOSTAT
> &THERMAL_REGION
> &PRINT
> &TEMPERATURE
> &EACH
> MD 1
> &END EACH
> &END TEMPERATURE
> &END PRINT
> &END THERMAL_REGION
> &PRINT
> &ENERGY
> &EACH
> MD 1
> &END EACH
> &END ENERGY
> &END PRINT
> &END MD
>
> &PRINT
> &RESTART
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
>
> &TRAJECTORY LOW
> FORMAT DCD
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &VELOCITIES OFF
> &END VELOCITIES
> &FORCES
> &END FORCES
> &END PRINT
> &END MOTION
>
> &FORCE_EVAL
> METHOD QS
>
> &DFT
> &SCF
> SCF_GUESS ATOMIC
> EPS_SCF 1.0E-7
> MAX_SCF 5000
> &OUTER_SCF
> MAX_SCF 10
> &END OUTER_SCF
> &OT
> # Mingshun's scheme for PM6
> PRECONDITIONER FULL_SINGLE_INVERSE
> MINIMIZER DIIS
> N_DIIS 9
> &END OT
> &PRINT
> &RESTART
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END SCF
>
> &QS
> METHOD PM3
> # My scheme
> EPS_DEFAULT 1.0E-12
> EXTRAPOLATION ASPC
> EXTRAPOLATION_ORDER 3
> &SE
> # &PARAMETER
> # @INCLUDE PARAM
> # &END PARAMETER
> &COULOMB
> CUTOFF 10.0
> RC_RANGE 0.5
> # RC_TAPER 2
> &END COULOMB
> &SCREENING
> RC_RANGE 0.5
> &END SCREENING
> &LR_CORRECTION
> CUTOFF 6.0
> RC_RANGE 0.5
> &END LR_CORRECTION
> &EXCHANGE
> CUTOFF 8.0
> RC_RANGE 0.5
> &END EXCHANGE
> &END SE
> &END QS
> &MGRID
> COMMENSURATE
> # CUTOFF 280
> &END MGRID
> &POISSON
> POISSON_SOLVER PERIODIC
> PERIODIC XYZ
> &EWALD
> &MULTIPOLES
> MAX_MULTIPOLE_EXPANSION QUADRUPOLE
> &END MULTIPOLES
> EWALD_TYPE EWALD
> ALPHA 0.5
> GMAX 31
> &END EWALD
> &END POISSON
>
> &PRINT
> &E_DENSITY_CUBE
> &EACH
> MD 1
> &END EACH
> &END E_DENSITY_CUBE
> &END PRINT
> &END DFT
>
> &SUBSYS
> &CELL
> ABC 12.4138 12.4138 12.4138
> PERIODIC XYZ
> &END CELL
> &COORD
> ........................................
> .........................................
> ........................................
> .......................................
> ........................................
> &END COORD
> &END SUBSYS
> &END FORCE_EVAL
>
>
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