bond problem
John
johnb... at gmail.com
Sat Apr 4 21:41:11 UTC 2009
Dear all,
I'm trying to reproduce Blumberger & Sprik’s article. “Quantum versus
classical electron transfer energy as reaction coordinate for aqueous
Ru2+/Ru3+ redox reaction” I want to calculate Ru2+ and Ru3+ separately. I
am stuck in this file.
-------------------------------------------------------------------------
&FORCE_EVAL
METHOD QS
&DFT
LSD
CHARGE +2
BASIS_SET_FILE_NAME ~/bin/GTH_BASIS1
POTENTIAL_FILE_NAME ~/bin/GTH_POTENTIALS
&SCF
SCF_GUESS ATOMIC
&END SCF
&XC
&XC_FUNCTIONAL
&LYP
&END
&BECKE88
&END
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.860 9.860 9.860
UNIT ANGSTROM
&END CELL
&TOPOLOGY
CONNECTIVITY GENERATE
&GENERATE
CREATE_MOLECULES
&END GENERATE
COORD_FILE_FORMAT OFF
&END TOPOLOGY
&COORD
Fe -2.8799089789 4.4833993160 -0.9253798435
O -4.5590653502 4.9284583342 -0.0621601829
H -4.9705923716 4.3640441785 0.6893891668
H -5.3164182399 5.5362415756 -0.2538566219
O -6.3299935050 4.6501002553 -3.2165611248
H -6.2549146971 3.6508586162 -3.3792673655
H -6.9156034477 4.8348081172 -3.9501089172
O -2.2309178755 1.9923408769 2.7645911766
H -2.1565313777 1.2884476066 3.3749391873
H -2.9197925757 2.4899670577 3.2035338211
O -6.0770832172 -2.7231315785 -9.5448709624
H -6.6824231738 -1.9822385218 -9.4211280474
H -5.9382474726 -3.0338301873 -8.6189155739
O -1.5590539933 8.4581237145 2.8351416768
H -0.7014554610 8.2291741700 2.4524975037
H -2.0130061115 8.5474909348 1.9935461408
O 9.2452622342 -5.2016109500 5.4580407027
H 9.0803631056 -5.7141148150 4.6416799086
H 9.9239068093 -4.6374143187 5.0948223542
O -2.2747965553 -3.6412773460 -0.5034106904
H -1.3309475835 -3.3368322136 -0.4927701592
H -2.6785712553 -2.7337453156 -0.3003969352
O -5.0150050737 -6.7585442027 1.9265699321
H -5.1775069842 -7.7010260951 1.7351149107
H -5.8697740333 -6.3925551219 2.1581907946
O 0.8447530721 6.9676594900 11.9177287714
H 1.7073334916 7.3677191845 11.6947056467
H 0.6518913920 6.5141851347 11.1177738640
O 6.0591575870 2.6714044751 -1.4726489030
H 5.3474665764 2.0757487291 -1.1127385014
H 6.4466468961 2.0834641415 -2.1735884409
O 3.4899901096 -1.6971208479 -4.9827700523
H 3.7505437278 -2.0037236132 -5.8540717308
H 4.1006777437 -2.1268748806 -4.4328135502
O -1.9498492896 3.8218715791 0.7845270001
H -1.5328361779 4.4385739266 1.4442998839
H -2.0488871006 2.9605980239 1.2847914463
O 0.9321859840 -7.8126933636 -7.4250105857
H 0.0329414295 -8.0583782013 -7.5266562638
H 1.1486171832 -8.1200037817 -6.5120872061
O -1.2177439540 3.9800638489 -1.8131933683
H -0.6840991767 3.1313826129 -1.5906664292
H -0.9145330384 4.0982865398 -2.7613003118
O -3.3284227931 -1.8974729757 7.2635935278
H -2.4263964010 -1.6247806670 6.8788457601
H -3.8045549804 -1.0362892279 7.1060434158
O 3.1479370099 -0.6458937922 -2.5276483725
H 3.3884480789 -0.8514820589 -3.4557508136
H 3.6344722272 -1.3774434262 -2.0751013265
O 7.1879953337 -8.9239121082 -13.3442298597
H 6.8446671365 -8.5711562075 -14.1613048318
H 7.7254300021 -9.6624243506 -13.7044807394
O -8.6023482493 -3.3193550929 -5.1537580676
H -8.7819195227 -3.1689491809 -6.1212676794
H -7.8410327266 -2.7039484048 -4.9109258801
O -1.6312805667 5.5167292375 -6.9923342866
H -0.8056792472 5.7540718563 -6.5608867815
H -2.1505132312 6.3409324352 -7.1702717642
O -1.1599325173 -1.2492174249 5.5835548423
H -0.5586672445 -2.0053137874 5.5852786019
H -1.2162000273 -1.1965002980 4.5769153998
O 0.4507584677 1.9022651399 8.0400381780
H 0.3803588966 1.5946413528 7.1350748078
H 0.7456410323 1.1634439653 8.5439230412
O 2.3267512174 -0.6727042425 1.1854652355
H 2.5458646034 0.0652573671 1.7955595250
H 1.4034743190 -0.7956305233 1.3884420398
O 6.5672661690 -1.0984518909 0.4890215160
H 6.6148451731 -0.1508625403 0.5933987343
H 5.6183713508 -1.1822689592 0.6206551821
O 13.8241697211 1.1652120167 -0.1672218219
H 13.2121429387 1.9116181141 -0.2940170580
H 13.1950907565 0.4365600472 -0.0399679561
O -7.4988319221 -5.5555520991 1.8185232839
H -7.3837127821 -5.7699475363 0.8563643360
H -8.1964989733 -6.1053099532 2.1088034849
O 3.2659641904 1.9791770773 6.1150563807
H 3.4940757601 1.1736027719 6.5963750850
H 2.3515019134 1.7588235846 5.7327525956
O 10.6859668444 0.9023905651 5.3551106427
H 9.8594127269 0.4030003706 5.2356781202
H 11.1491058894 0.1555256165 5.7681348240
O 0.3760363101 -3.1586261422 -0.8543017938
H 0.5403724685 -2.2421497891 -0.9851024800
H 1.2122330106 -3.5814031598 -1.0268333285
O 5.5807230240 -7.1801081002 -5.1191205524
H 5.3360212979 -6.4482539508 -5.7290439438
H 4.6785146465 -7.5446958824 -4.8933286755
O 2.6572577924 3.6535389336 -0.8327578995
H 2.9537750589 4.1567130338 -1.6386441686
H 1.8520090260 3.2252090800 -1.1268435488
O -5.8148422292 -3.3672919847 2.9400281976
H -6.4576770992 -4.0665517099 3.0231423099
H -5.0407848682 -3.8319856458 3.2242012598
O 6.1901471261 5.2539472758 -2.5686945148
H 5.3182543979 5.0205417149 -2.9790688482
H 6.2705281827 6.1021482659 -3.1176707935
&END COORD
&KIND RU
BASIS_SET DZV-GTH
POTENTIAL GTH-PADE-q8
&END KIND
&KIND H
BASIS_SET DZV-GTH
POTENTIAL GTH-BP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-BP-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PREFERRED_FFT_LIBRARY FFTSG
EXTENDED_FFT_LENGTHS T
PROJECT test
RUN_TYPE GEO_OPT
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 10000
TIMESTEP 1.0
TEMPERATURE 300.0
&THERMOSTAT
REGION GLOBAL
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END
&PRINT
&ENERGY
&EACH
MD 10
&END EACH
&END ENERGY
&END PRINT
&END MD
&PRINT
&TRAJECTORY
&EACH
MD 10
&END EACH
&END TRAJECTORY
&END PRINT
&END MOTION
-------------------------------------
Thanks in advance
John
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