[CP2K-user] [CP2K:18384] Re: Getting wrong Mulliken charges for thiols on gold surface system
Vikash Khokhar
vikashkhokhar141 at gmail.com
Wed Jan 25 11:15:11 UTC 2023
Thanks, Victor, for your kind reply and suggestions.
My apologies for mentioning the 'wrong Mulliken charges.' I just wanted to
know why I was getting unreasonable charges for my system, was I missing
something.
I'll try your suggestions and will get back to you.
Please let me know if I'm missing something in my calculations to compute
reasonable charges for the metallic systems!
Thank you
Vikash
On Monday, January 23, 2023 at 4:00:46 PM UTC+5:30 volk... at gmail.com wrote:
> Good day, Vikash.
> According to my knowledge and experience,
> classification "wrong Mulliken"
> does not sound right.
>
> The Mulliken protocol is as described in literature.
> There are many publications to report when it was very helpful and
> when it did not bring numbers consistent with the experimental.
>
> The approach by Robert Mulliken (I graduated from the lab which stemmed
> from his)
> was discussed to contradict experimental anticipations when in systems
> with metals.
> You have to explore literature on your own.
>
> This does not mean that it would compute "wrong Mulliken".
> There are other protocols with own benefits and lacks.
>
> In general, computing one set of charges for a system does not have a
> strong value.
> Instead, comparing how charges would change when you explore various
> relevant
> systems using the same level of theory may be scientific.
>
> You may try RESP as a complimentary approach.
> Perhaps, the developers and other users would be kind enough
> to update this reply if I made a mistake.
>
> Victor
>
> &PROPERTIES
> &RESP
> USE_REPEAT_METHOD
> &SPHERE_SAMPLING
> AUTO_VDW_RADII_TABLE UFF
> AUTO_RMIN_SCALE 1.0
> AUTO_RMAX_SCALE 10
> &END
> &PRINT
> &RESP_CHARGES_TO_FILE
> FILENAME resp.dat
> &EACH
> MD 1
> &END EACH
> &END RESP_CHARGES_TO_FILE
> &END PRINT
> &END RESP
> &FIT_CHARGE
> &END FIT_CHARGE
> &END PROPERTIES
> &END FORCE_EVAL
>
>
> On Sat, Jan 21, 2023 at 5:21 PM Vikash Khokhar <vikashkh... at gmail.com>
> wrote:
>
>> Anybody please answer this question?
>>
>> On Wednesday, January 18, 2023 at 12:39:06 PM UTC+5:30 Vikash Khokhar
>> wrote:
>>
>>> Sorry for the mistake.
>>> I mentioned, 'But S atoms should have +ve charge,' but it was 'S atoms
>>> should have -ve charge.'
>>> On Wednesday, January 18, 2023 at 12:34:41 PM UTC+5:30 Vikash Khokhar
>>> wrote:
>>>
>>>> Hi CP2K community,
>>>>
>>>> I'm optimizing Au (111) 5 layers surface with aromatic thiols on the
>>>> surface.
>>>> But the charge on S atoms is +ve, and the first and last layers of Au
>>>> have -ve charge.
>>>> But S atoms should have +ve charge.
>>>>
>>>> Please suggest how I can get the correct charges.
>>>>
>>>> I have attached the Mulliken charges file and the coordinates file
>>>> here, just in case you'd like to have a look.
>>>>
>>>> The input file is -
>>>>
>>>> --------------------------------------------------------------------------------------------------------------------------------------------
>>>> &GLOBAL
>>>> PROJECT Au_2DMBT_tilt
>>>> RUN_TYPE GEO_OPT
>>>> PRINT_LEVEL MEDIUM
>>>> &END GLOBAL
>>>>
>>>> &MOTION
>>>> &GEO_OPT
>>>> TYPE MINIMIZATION
>>>> OPTIMIZER BFGS
>>>> MAX_DR 3.00E-03
>>>> MAX_FORCE 4.50E-04
>>>> RMS_DR 1.50E-03
>>>> RMS_FORCE 3.00E-04
>>>> MAX_ITER 3000
>>>> &END GEO_OPT
>>>>
>>>> &CONSTRAINT
>>>> &FIXED_ATOMS
>>>> COMPONENTS_TO_FIX XYZ
>>>> LIST 1..48
>>>> &END FIXED_ATOMS
>>>> &END CONSTRAINT
>>>>
>>>> &END MOTION
>>>>
>>>> &FORCE_EVAL
>>>> METHOD QS
>>>>
>>>> &DFT
>>>> BASIS_SET_FILE_NAME
>>>> /home/spremkumar.iitm/vikash/cp2k_pot/BASIS_MOLOPT
>>>> POTENTIAL_FILE_NAME
>>>> /home/spremkumar.iitm/vikash/cp2k_pot/GTH_POTENTIALS
>>>>
>>>> &QS
>>>> METHOD GPW
>>>> EXTRAPOLATION USE_GUESS
>>>> EPS_DEFAULT 1.0E-10
>>>> &END QS
>>>>
>>>> &MGRID
>>>> CUTOFF 500
>>>> NGRIDS 4
>>>> REL_CUTOFF 60
>>>> &END MGRID
>>>>
>>>> &SCF
>>>> SCF_GUESS ATOMIC
>>>> EPS_SCF 1.0E-05
>>>> MAX_SCF 200
>>>> ADDED_MOS 10
>>>>
>>>> &DIAGONALIZATION T
>>>> ALGORITHM STANDARD
>>>> &END DIAGONALIZATION
>>>>
>>>> &SMEAR ON
>>>> METHOD FERMI_DIRAC
>>>> ELECTRONIC_TEMPERATURE [K] 300
>>>> &END SMEAR
>>>>
>>>> &MIXING T
>>>> METHOD BROYDEN_MIXING
>>>> ALPHA 0.4
>>>> NBROYDEN 8
>>>> &END MIXING
>>>> &END SCF
>>>>
>>>> &XC
>>>> &XC_FUNCTIONAL PBE
>>>> &END XC_FUNCTIONAL
>>>>
>>>> &vdW_POTENTIAL
>>>> DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>>> &PAIR_POTENTIAL
>>>> PARAMETER_FILE_NAME
>>>> /home/spremkumar.iitm/vikash/cp2k_pot/dftd3.dat
>>>> TYPE DFTD3
>>>> REFERENCE_FUNCTIONAL PBE
>>>> R_CUTOFF 25.0
>>>> &END PAIR_POTENTIAL
>>>> &END vdW_POTENTIAL
>>>> &END XC
>>>>
>>>> &KPOINTS
>>>> SCHEME MONKHORST-PACK 2 3 1
>>>> FULL_GRID .TRUE.
>>>> PARALLEL_GROUP_SIZE 0
>>>> &END KPOINTS
>>>>
>>>> &END DFT
>>>>
>>>> &SUBSYS
>>>> &CELL
>>>> PERIODIC XYZ
>>>> A 17.3099747000000015 0.0000000000000000
>>>> 0.0000000000000000
>>>> B 0.0000000000000000 9.9939184000000001
>>>> 0.0000000000000000
>>>> C 0.0000000000000000 0.0000000000000000
>>>> 35.0000000000000000
>>>> &END CELL
>>>>
>>>> &COORD
>>>> @INCLUDE Au_2DMBT_tilt.xyz
>>>> &END COORD
>>>>
>>>> &KIND Ag
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>> POTENTIAL GTH-PBE
>>>> &END KIND
>>>> &KIND Au
>>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>>> POTENTIAL GTH-PBE
>>>> &END KIND
>>>> &KIND H
>>>> BASIS_SET DZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE
>>>> &END KIND
>>>> &KIND C
>>>> BASIS_SET DZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE
>>>> &END KIND
>>>> &KIND S
>>>> BASIS_SET DZVP-MOLOPT-GTH
>>>> POTENTIAL GTH-PBE
>>>> &END KIND
>>>>
>>>> &END SUBSYS
>>>>
>>>> --------------------------------------------------------------------------------------------------------------------------------------------
>>>>
>>>> Thank you
>>>> Vikash Khokhar
>>>> Project Assistant
>>>> Pradeep research group,
>>>> DST Unit of Nanoscience & Thematic Unit of Excellence,
>>>> Department of Chemistry
>>>> Indian Institute of Technology Madras, Chennai, India
>>>> Web: pradeepresearch.org
>>>>
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