[CP2K:6254] Energy conservation in periodic QM/MM
Jonggu Jeon
jeonj... at gmail.com
Wed Mar 18 11:22:10 UTC 2015
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 <javascript:>>:
>
>> 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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