Hi I am sorry. That's true. I tried iron, it didn't work also. I pasted wrong xyz coordinate. It could be like this. > Ru -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 ...... ..... ...... that's error report: ------------------------------------------------ ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): 441.893460017026825 * * *** 20:50:57 ERRORL3 in thermostat_utils:communication_thermo_low1 *** *** processor 0 err=-300 condition FAILED at line 1485 *** * * ===== Routine Calling Stack ===== 2 qs_mol_dyn_low 1 CP2K CP2K| condition FAILED at line 1485 CP2K| Abnormal program termination, stopped by process number 0 -------------------------------------------------------- regards <div class="gmail_quote">On Sun, Apr 5, 2009 at 1:42 PM, Juerg Hutter <<a href="mailto:hut...@pci.uzh.ch" target="_blank">hut...@pci.uzh.ch</a>> wrote: <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi <div> &COORD Fe -2.8799089789 4.4833993160 -0.9253798435 </div>I thought you wanted to calculate Ru? regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Physical Chemistry Institute FAX : ++41 44 635 6838 University of Zurich E-mail: <a href="mailto:hut...@pci.uzh.ch" target="_blank">hut...@pci.uzh.ch</a> Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- <div><div></div><div> On Sat, 4 Apr 2009, John wrote: > 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 > > > > </div></div><div><div></div><div> </div></div></blockquote></div>