[CP2K:5357] Temperature increased during CONSTRAINT MD calculation
bharat
bharats... at gmail.com
Wed Jun 4 16:35:01 UTC 2014
Hello Juerg,
Thank you. Using default Poisson solver resolved the issue.
One quick question: What is the unit of "Shake Lagrangian Multipliers"
which is printed in .LagrangeMultLog file? Is Shake value just an average
of Lagrange parameter <λ> or it is f(q) = <λ>-2*KB*T/q where KB
is Boltzmann constant and q is mechanical constraint?
Thank you.
Bharat
On Tuesday, June 3, 2014 9:30:16 AM UTC-4, jgh wrote:
>
> Hi
>
> just a few quick tips:
>
> - equilibrate your system using an appropritae thermostate.
> You might have to do this for every constraint setting
> - use NVE or NVT ensemble, not Langevin (needs special settings)
> - Use default Poisson solver (delete that section if not needed)
>
> regards
>
> Juerg
>
> --------------------------------------------------------------
> Juerg Hutter Phone : ++41 44 635 4491
> Institut für Chemie C FAX : ++41 44 635 6838
> Universität Zürich E-mail: hut... at chem.uzh.ch
> <javascript:>
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com <javascript:> wrote: -----
> To: cp... at googlegroups.com <javascript:>
> From: bharat
> Sent by: cp... at googlegroups.com <javascript:>
> Date: 06/03/2014 01:28AM
> Subject: [CP2K:5357] Temperature increased during CONSTRAINT MD
> calculation
>
> Dear C2PK experts,
>
> I am trying to do constraint MD calculation for the purpose of PMF
> calculation. I used the ENSEMBLE as LANGEVIN and switched on the Lagrange
> Multiplier. Since my system has Zn atom, I used MOLOPT basis sets for all
> atoms (Zn, O, and H). First I performed few steps of geometry optimization
> to obviate bad contacts. But the problem is temperature of the system
> increased too much and calculation is very slow. I changed different
> PRECONDITIONERs too but does not help. I assume that something is going
> really bad in the input file.
>
> Can anyone correct me where I am going wrong?
>
> Thank you in advance.
>
> Sincerely,
> Bharat
>
> INPUT:
> @SET CURR_I 01
>
> @SET REPLICA 001
> !@SET SEED 2000
>
> &GLOBAL
> PROGRAM_NAME CP2K
> PROJECT_NAME Zn-31H2O_${REPLICA}_${CURR_I}
> RUN_TYPE MD
> ! SEED ${SEED}
> PREFERRED_FFT_LIBRARY FFTW
> PRINT_LEVEL LOW
> SAVE_MEM
> &END GLOBAL
> &FORCE_EVAL
> METHOD QS
>
> &DFT
> BASIS_SET_FILE_NAME ./BASIS_MOLOPT
> POTENTIAL_FILE_NAME ./POTENTIAL
> CHARGE 2
> # MULTIPLICITY 1
>
> &SCF
> SCF_GUESS ATOMIC
> EPS_SCF 1.0E-6
> MAX_SCF 50
> &OUTER_SCF
> MAX_SCF 10
> &END OUTER_SCF
> &OT
> # My scheme
> PRECONDITIONER FULL_SINGLE_INVERSE
> MINIMIZER DIIS
> N_DIIS 7
> &END OT
> &PRINT
> &RESTART
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
> &END PRINT
> &END SCF
>
> &QS
> METHOD GAPW
> # My scheme
> EPS_DEFAULT 1.0E-12
> &END QS
> &MGRID
> COMMENSURATE
> CUTOFF 300
> &END MGRID
> &POISSON
> POISSON_SOLVER MULTIPOLE
> PERIODIC NONE
> &MULTIPOLE
> RCUT 40
> &END MULTIPOLE
> &END POISSON
>
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &XC_GRID
> XC_SMOOTH_RHO NN10
> XC_DERIV SPLINE2_SMOOTH
> &END XC_GRID
> &END XC
>
> &PRINT
> &E_DENSITY_CUBE
> &EACH
> MD 20
> &END EACH
> &END E_DENSITY_CUBE
> &END PRINT
> &END DFT
> &SUBSYS
> &CELL
> ABC 9.865 9.865 9.865
> &END CELL
> # basis set and pseudopotential START
> &KIND O
> BASIS_SET DZVP-MOLOPT-SR-GTH-q6
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &KIND H
> BASIS_SET DZVP-MOLOPT-SR-GTH-q1
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND Zn
> BASIS_SET DZVP-MOLOPT-SR-GTH-q12
> POTENTIAL GTH-BLYP-q12
> &END KIND
> # basis set and pseudopotential END
> &COORD
> Zn 5.7424793053 5.7794839244 4.5947129958
> O 8.1467217278 4.6850039781 3.1371317724
> H 8.6190715739 3.7975262203 3.0436809498
> H 8.8834641536 5.2988681112 3.4025380140
> O 10.3950115644 6.0303774461 4.0310716263
> H 10.7901584379 5.2672666136 4.5352088693
> H 10.3495569218 6.7612577065 4.6892301032
> O 7.6704674012 3.8407666568 7.7762877652
> H 8.5229361417 3.3708133953 7.5345459917
> H 7.6044435245 3.9237085873 8.7514863491
> O 6.3073913259 5.7915461691 6.5866515381
> H 5.5936672631 5.9792325455 7.2414994267
> H 6.8603152838 5.0571620794 6.9853734612
> O -0.0319244016 2.5908838992 6.8946112084
> H 0.6036495000 2.9941643303 6.2452864909
> H 0.3692405728 1.7576666162 7.1969200999
> O 4.6930130988 5.1084064995 8.8465406634
> H 4.0618447281 5.6903810851 9.3092238490
> H 5.3235555146 4.7978119585 9.5286898344
> O 9.8241320271 7.3561454459 6.4654122261
> H 9.4551523831 8.2667345654 6.5499208550
> H 9.0609931436 6.7919468532 6.6946065211
> O 3.4389459231 3.1383762018 7.2306023067
> H 3.8322278004 3.8936103039 7.7340685331
> H 4.2360809719 2.6157312182 6.9492389101
> O 4.8465044101 3.9854075872 4.5392996083
> H 5.3167050351 3.1516989562 4.7627388838
> H 4.4394356786 3.8672542636 3.6167814896
> O 2.2137360835 6.1537354012 7.6435483583
> H 1.9132157849 5.5727770830 8.3648434598
> H 1.4014762451 6.6139569603 7.3249297506
> O 4.9923344152 9.2326241471 1.1310295566
> H 4.9854355107 10.1816572735 0.8509544771
> H 5.8226299353 9.1646514633 1.6540806276
> O 1.7888589587 3.8463829901 5.1779622339
> H 2.5236279358 3.6733461191 5.8471123730
> H 2.0328935059 3.3509245636 4.3728855968
> O 5.2491177949 2.0432352767 10.2132223879
> H 5.5933691612 2.2513673559 11.1354023660
> H 4.3989001902 2.5105798343 10.1143407515
> O 3.8542965301 6.6640849318 4.9223951284
> H 3.1122704243 6.0291676508 4.8822823335
> H 3.6116875155 7.4420472996 4.3821571950
> O 3.6234603335 3.8842833429 2.2086274308
> H 3.0329902975 3.0789231735 2.1413451069
> H 3.0673108331 4.6739570086 2.0114691713
> O 6.1759571955 2.1633065016 2.8905487887
> H 6.7691443935 2.9183810528 3.0642343036
> H 6.7290306617 1.3351328054 2.9879034353
> O 9.9843360019 8.9081599493 2.2941640612
> H 10.9111338034 9.0596075827 2.5911502523
> H 10.0380427767 8.9455563793 1.3232051481
> O 2.9407951261 9.1153733246 2.8117419346
> H 3.2922947796 9.3425985799 3.7238095082
> H 3.7468412154 9.1314864063 2.1935025475
> O 2.0194237391 1.7848766417 2.0880218254
> H 1.8629424145 1.8295569013 1.1093120382
> H 2.3458536172 0.8693952658 2.3049980117
> O 2.3414304177 6.4044072884 1.8254884894
> H 2.6261184123 7.3296810321 1.9951462463
> H 1.5734985823 6.3086148009 2.4416645204
> O 4.0380636525 9.5976928078 5.2054182216
> H 4.0758588766 9.1013798352 6.0722577969
> H 4.6951449245 10.3121916363 5.2578339004
> O 5.9068151590 2.1040678337 6.4267067871
> H 6.0950410161 1.3209852009 6.9840507111
> H 6.5007725646 2.7854400173 6.8411501215
> O 7.7825452374 9.2315282060 6.2923279682
> H 7.7799905238 10.0146288780 5.7073486957
> H 7.3013368849 9.5223896794 7.1085919635
> O 6.6513045466 0.4370729781 8.5660372075
> H 7.1766746167 -0.0328785361 9.2347224690
> H 6.1103376191 1.0910758216 9.0923920638
> O 7.4031209602 9.6289887597 2.8331458763
> H 8.3890965438 9.5618684815 2.7200055706
> H 7.1744168703 8.8656637144 3.4099474113
> O 4.2035921186 8.1478750411 7.5260128932
> H 3.4717566018 7.4874518908 7.6170113618
> H 4.3109788206 8.5752770575 8.3965546887
> O 1.7417197736 2.5959202025 9.3303494745
> H 0.9372666067 3.0188154608 8.9784353351
> H 2.3740569008 2.6289933655 8.5606682435
> O 7.1518683812 7.3643554477 4.4700633544
> H 7.2254058666 7.8959889353 5.3203099956
> H 8.0519945221 7.0192050374 4.3092210426
> O 9.2544136926 2.3505594908 2.5422868142
> H 9.0662504852 2.2911860884 1.5880890304
> H 10.2190720764 2.1183446316 2.6040201598
> O 5.4344301186 6.2919890147 2.4871048625
> H 6.0413342023 5.9312556336 1.7942947850
> H 4.5298233648 6.0932835753 2.1706884266
> O 7.2593392544 5.1069008467 10.4736873287
> H 7.6824697185 4.9255222432 11.3724141357
> H 7.7677403524 5.8463732646 10.0905029617
> &END COORD
> ! ######################################## Basis sets and
> pseudopotentials
> &COLVAR
> &DISTANCE
> ATOMS 11 13
> &END DISTANCE
> &END COLVAR
> &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
> &MD
> ENSEMBLE LANGEVIN
> STEPS 2000
> TIMESTEP 0.5
> TEMPERATURE 300.0
> &THERMOSTAT
> TYPE NOSE
> ! REGION GLOBAL
> &NOSE
> TIMECON [wavenumber_t] 2000
> &END NOSE
> &END THERMOSTAT
> &PRINT ON
> &ENERGY
> &EACH
> MD 1
> &END EACH
> ! FILENAME =${BASE_NAME}-${ID}.ener
> &END ENERGY
> &END PRINT
> &END MD
> &PRINT
> &RESTART
> &EACH
> MD 1
> &END EACH
> &END RESTART
> &RESTART_HISTORY OFF
> &END RESTART_HISTORY
>
> &TRAJECTORY SILENT
> FORMAT DCD
> &EACH
> MD 1
> &END EACH
> &END TRAJECTORY
> &VELOCITIES OFF
> &END VELOCITIES
> &FORCES OFF
> &END FORCES
> &END PRINT
> &CONSTRAINT
> SHAKE_TOLERANCE 1.0E-9
> &LAGRANGE_MULTIPLIERS ON
> COMMON_ITERATION_LEVELS 3
> &END LAGRANGE_MULTIPLIERS
> &COLLECTIVE
> COLVAR 1
> INTERMOLECULAR T
> TARGET [angstrom] 1.0
> &END COLLECTIVE
> &END CONSTRAINT
> &END MOTION
> ! &EXT_RESTART
> ! RESTART_FILE_NAME ./water_001_01-1.restart
> ! &END EXT_RESTART
> --
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