[CP2K:6254] Energy conservation in periodic QM/MM
Matt W
MattWa... at gmail.com
Thu Mar 19 11:17:54 UTC 2015
Try increasing the cutoff to 600-800 Ry? BLYP functional is known to be
noisy.
I have repeated the QM/MM MD using MULTIPOLE OFF using the latest CP2K
> trunk binary (svn:15171). The total energy from this new run is *identical*
> to the previous one using MULTIPOLE section. The only difference is that
> the decoupling/recoupling energies and the warning messages about QM atoms
> close to the boundary are not printed in the output file any more.
>
> Dorothea pointed out that, _if_ your QM box is the same size as the QMMM
box (as you have in the input above), you don't need the de/recoupling - it
_should_ give identical results. It just slows the calculation a little.
HTH
Matt
> I have also tried the "CENTER_GRID T" keyword together with CENTER
> EVERY_STEP as Matt suggested above and its short time energy profile up to
> 100 fs is nearly the same as the one without CENTER_GRID. I guess the
> total energy is still adversely affected by the centering even with the
> CENTER_GRID.
>
> From these observations, I'm afraid it's likely that the current CP2K
> cannot handle gracefully the QM atoms crossing boundary.
> I'd appreciate any comment or suggestion.
>
> Jonggu
>
>
> 2015년 3월 18일 수요일 오후 9시 13분 29초 UTC+9, Matt W 님의 말:
>>
>> Hi,
>>
>> there is also the CENTER_GRID that has been introduced quite recently. I
>> don't know how much it has been tested, maybe someone else can comment? But
>> for my simple test water system it seems to improve the energy conservation
>> considerably. The idea is, I think, to only center the QM molecule in a
>> "quantized" manner on equivalent grid points of the (fine DFT?) grid.
>>
>> To get really good energy conservation you might need to increase your
>> cutoff/rel_cutoff too.
>>
>> Matt
>>
>> On Wednesday, March 18, 2015 at 11:22:10 AM UTC, Jonggu Jeon wrote:
>>>
>>> Dear Dorothea,
>>>
>>> Thank you for the invaluable suggestion.
>>> While your answer makes perfect sense to me, I just found out that CP2K
>>> 2.5.1 does not have option to turn off QMMM/PERIODIC/MULTIPOLE using the
>>> section parameter OFF.
>>> Therefore, CP2K 2.5.1 produces the same (diverging) energy profile
>>> whether I set &MULTIPOLE OFF or not.
>>>
>>> I will install version 2.6 and try it again.
>>>
>>> Best regards,
>>>
>>> Jonggu
>>>
>>>
>>> 2015년 3월 18일 수요일 오후 6시 22분 40초 UTC+9, Dorothea Golze 님의 말:
>>>>
>>>> Hi,
>>>>
>>>> if you have a fully periodic setup where the QM and MM boxes are equal,
>>>> you do not need the decoupling/recoupling stuff, i.e. switch off explicitly
>>>> the MULTIPOLE section like that
>>>> &MULTIPOLE OFF
>>>> &END
>>>>
>>>> Also set in the QMMM section
>>>>
>>>> &WALLS
>>>> TYPE NONE
>>>> &END WALLS
>>>>
>>>> That should address your first question...
>>>>
>>>> Cheers,
>>>> Dorothea
>>>>
>>>>
>>>> 2015-03-18 8:46 GMT+01:00 Jonggu Jeon <jeon... at gmail.com>:
>>>>
>>>>> Dear CP2K users,
>>>>>
>>>>> I'd like to ask some questions on the capabilities of the QM/MM part
>>>>> of CP2K (I'm using version 2.5.1, svn:13632).
>>>>>
>>>>> I've been attempting a QM/MM MD simulation with CP2K. My system
>>>>> consists of one NMA molecule (TZV2P/BLYP DFT) and 48 methanol molecules
>>>>> (OPLS MM force field).
>>>>> The relevant parts of my input file are attached at the end of the
>>>>> message. Basically, I'm following all the advices from this group for a
>>>>> fully periodic QM/MM setup and set the cell sizes for the QM (in QMMM/CELL)
>>>>> and MM (in SUBSYS/CELL) parts equal.
>>>>>
>>>>> The following is the summary of my findings.
>>>>>
>>>>> 1. With FORCE_EVAL/QMMM/CENTER EVERY_STEP, the total energy is not
>>>>> conserved, as pointed out by Dr. Laino in this group before.
>>>>> 2. With FORCE_EVAL/QMMM/CENTER SETUP_ONLY, the total energy is very
>>>>> well conserved within 0.1 kcal/mol for a few ps until the QM molecule
>>>>> eventually crosses the cell boundary. At this point system energy shoots
>>>>> up by several kcal/mol and the output begins to produce the following
>>>>> messages:
>>>>>
>>>>> *** 16:11:03 WARNING in qmmm_util:apply_qmmm_walls_reflective :: One
>>>>> or ***
>>>>> *** few QM atoms are within the SKIN of the quantum box. Check your
>>>>> run ***
>>>>> *** and you may possibly consider: the activation of the QMMM
>>>>> WALLS ***
>>>>> *** around the QM box, switching ON the centering of the QM box
>>>>> or ***
>>>>> *** increase the size of the QM cell. CP2K CONTINUE but results could
>>>>> be ***
>>>>> *** meaningless. qmmm_util.F line
>>>>> 206 ***
>>>>>
>>>>> My questions are as follows:
>>>>>
>>>>> 1. Is it possible to achieve the energy conservation in a fully
>>>>> periodic DFT/MM MD without worrying about the QM molecule crossing the cell
>>>>> boundary? I believe this is possible in full DFT MD but my experience on
>>>>> CP2K QM/MM so far indicates otherwise. I'd appreciate if someone can
>>>>> provide an answer and keywords to achieve it.
>>>>>
>>>>> 2. The QMMM/CENTER option affects energy conservation a lot. When
>>>>> CENTER EVERY_STEP is used, would it improve energy conservation if I use
>>>>> finer grids by increasing DFT/MGRID/CUTOFF value?
>>>>>
>>>>> The skeletal form of my input file is attached below.
>>>>> Thank you.
>>>>>
>>>>> Jonggu Jeon
>>>>>
>>>>>
>>>>>
>>>>> &MOTION
>>>>> &MD
>>>>> ENSEMBLE NVE
>>>>> STEPS 40000
>>>>> TIMESTEP 0.5
>>>>> STEP_START_VAL 0
>>>>> TIME_START_VAL 0
>>>>> &END MD
>>>>> &END MOTION
>>>>> &FORCE_EVAL
>>>>> METHOD QMMM
>>>>> &DFT
>>>>> BASIS_SET_FILE_NAME /opt/cp2k/2.5.1/tests/QS/GTH_BASIS_SETS
>>>>> POTENTIAL_FILE_NAME /opt/cp2k/2.5.1/tests/QS/POTENTIAL
>>>>> WFN_RESTART_FILE_NAME wfn.rst
>>>>> CHARGE 0
>>>>> &SCF
>>>>> MAX_SCF 30
>>>>> EPS_SCF 9.9999999999999995E-07
>>>>> SCF_GUESS RESTART
>>>>> &OT T
>>>>> MINIMIZER DIIS
>>>>> PRECONDITIONER FULL_ALL
>>>>> ENERGY_GAP 1.0000000000000000E-03
>>>>> &END OT
>>>>> &OUTER_SCF T
>>>>> EPS_SCF 9.9999999999999995E-07
>>>>> MAX_SCF 1
>>>>> &END OUTER_SCF
>>>>> &END SCF
>>>>> &QS
>>>>> EPS_DEFAULT 1.0000000000000000E-10
>>>>> MAP_CONSISTENT T
>>>>> EXTRAPOLATION ASPC
>>>>> EXTRAPOLATION_ORDER 3
>>>>> METHOD GPW
>>>>> &END QS
>>>>> &MGRID
>>>>> CUTOFF 2.8000000000000000E+02
>>>>> COMMENSURATE T
>>>>> &END MGRID
>>>>> &XC
>>>>> &XC_GRID
>>>>> XC_SMOOTH_RHO NN50
>>>>> XC_DERIV SPLINE2_SMOOTH
>>>>> &END XC_GRID
>>>>> &XC_FUNCTIONAL NO_SHORTCUT
>>>>> &BECKE88 T
>>>>> &END BECKE88
>>>>> &LYP T
>>>>> &END LYP
>>>>> &END XC_FUNCTIONAL
>>>>> &VDW_POTENTIAL
>>>>> POTENTIAL_TYPE PAIR_POTENTIAL
>>>>> &PAIR_POTENTIAL
>>>>> TYPE DFTD3
>>>>> PARAMETER_FILE_NAME /opt/cp2k/2.5.1/tests/QS/dftd3.dat
>>>>> REFERENCE_FUNCTIONAL BLYP
>>>>> CALCULATE_C9_TERM F
>>>>> REFERENCE_C9_TERM F
>>>>> LONG_RANGE_CORRECTION F
>>>>> &END PAIR_POTENTIAL
>>>>> &END VDW_POTENTIAL
>>>>> &END XC
>>>>> &END DFT
>>>>> &MM
>>>>> &FORCEFIELD
>>>>> PARMTYPE AMBER
>>>>> PARM_FILE_NAME ndmd48.ao.prmtop
>>>>> &SPLINE
>>>>> EMAX_SPLINE 1.0000000000000000E+00
>>>>> &END SPLINE
>>>>> &END FORCEFIELD
>>>>> &POISSON
>>>>> &EWALD
>>>>> EWALD_TYPE SPME
>>>>> ALPHA 3.4999999999999998E-01
>>>>> GMAX 18
>>>>> &END EWALD
>>>>> &END POISSON
>>>>> &END MM
>>>>> &QMMM
>>>>> E_COUPL GAUSS
>>>>> USE_GEEP_LIB 7
>>>>> NOCOMPATIBILITY T
>>>>> CENTER SETUP_ONLY
>>>>> INITIAL_TRANSLATION_VECTOR -1.0888775605157457E+01
>>>>> -2.9066675351256084E+00 7.3922596274008097E+00
>>>>> &CELL
>>>>> ABC 1.5084868700000001E+01 1.5084868700000001E+01
>>>>> 1.5084868700000001E+01
>>>>> PERIODIC XYZ
>>>>> &END CELL
>>>>> &PERIODIC
>>>>> GMAX 5.0000000000000000E-01
>>>>> &MULTIPOLE
>>>>> RCUT 1.2000000000000000E+01
>>>>> EWALD_PRECISION 4.9999999999999998E-07
>>>>> ANALYTICAL_GTERM T
>>>>> NGRIDS 50 50 50
>>>>> &END MULTIPOLE
>>>>> &END PERIODIC
>>>>> &END QMMM
>>>>> &SUBSYS
>>>>> &CELL
>>>>> A 1.5084868700000001E+01 0.0000000000000000E+00
>>>>> 0.0000000000000000E+00
>>>>> B 0.0000000000000000E+00 1.5084868700000001E+01
>>>>> 0.0000000000000000E+00
>>>>> C 0.0000000000000000E+00 0.0000000000000000E+00
>>>>> 1.5084868700000001E+01
>>>>> MULTIPLE_UNIT_CELL 1 1 1
>>>>> &END CELL
>>>>> &TOPOLOGY
>>>>> NUMBER_OF_ATOMS 156
>>>>> CONN_FILE_NAME ndmd48.ao.prmtop
>>>>> CONN_FILE_FORMAT AMBER
>>>>> MULTIPLE_UNIT_CELL 1 1 1
>>>>> &END TOPOLOGY
>>>>> &END SUBSYS
>>>>> &END FORCE_EVAL
>>>>>
>>>>> --
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>>>>>
>>>>
>>>>
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