[gmx-users] mdrun parallel problem

[hazizian]

hi 
when I run mdrun command every thing is Ok and the mdrun go ahead.
but when I use mpimdrun -np 4 mdrungromacs_mpi (parallel mode) for that 
system this error ocurres:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 10 and 13) rms nan
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      8      9   89.9    0.1530 
11592544602356690794149168969393760996239342775983893005516927983251097147504439292066638500426250705980813734229829975395000280373684744692586117711414671790656106859969345183771267950473240732416558265351622189865601502304032810619264349120069245281231012586079732268655183994835482866911123899154432.0000      
0.1530
      9     10   90.3    0.1470 
16036167880742354855096886906681843538849647477052938610862567924576497428925115902300799637356604784006164398089987940827677766417283738560721356490919424654904212022521433723175749194573864938678463377785200251111017472046674137050620340219568519409800691838265642224327335886969526288110734853275648.0000      
0.1470
     10     11   90.0    0.1000 
52138715047847071339688397636690346485935832919415405755885202754568562560002246286125668604765521956300310207712071652968529852596487658397321213178060799698018346730454676469004925033390729371136278122033451354247687371018718798330647215813356175429026574014180588619000863131392364778685918533910528.0000      
0.1000
     10     12   90.0    0.1000 
114971882772290785787816897723904446980550453167914318670481461692820991109213943578741728576393265151197090028849388897577039877327117035382874438763483892928219622259156403714219370717406919903063846337636188718726649830007774535386264456245458037264954639231686640463173310545508002086748078613725184.0000      
0.1000
     10     13   90.0    0.1000 
140388532442843521203676712870965976356435566746521148567473295562460087964114072085928527561252719351173924525283644081220767766664655967559865407875133411682821399590701404754548485879456552721182744977594948520661356523552274916746657606965996881357260397888105362183121693797618451556350857094103040.0000      
0.1000
     60     61   90.0    0.1000 
123894341988150221405121811896932818893441331171028392120102030517345363213224305513845788511258066129801795102432087571687356412265004013287745879063286984281442042014320426185710974126284090026602505146670421811693156353202149027930373701952135720481865470571481407086885580036112851315957541019582464.0000      
0.1000
     60     62   90.0    0.1000 
123053697440188603918882484403912976332767271299138580735814697393470885066586566460722042994768813026375927226034932604243114329976600158449949651667561887152650948582504893467259486823496665258176228833144591533069551989636985145767952531819902954529405474044912486707326334140162917832111002430210048.0000      
0.1000
     60     63   90.0    0.1000 
107552151225089259928025783342986804790918473428689484428404454953066276970886660370292284489629355510828679863766183431676382029478012130565245430275959617570735516520646151496804036692620558845162196686899442901979315949157427655647365081586987404052304500814215101276297069238548011240954695264501760.0000      
0.1000
    126    127   89.5    0.1330 
3206974911255019380523634860453433692365172784795547737090196304970624279317182554207516590965283201627397837991811681757439320247454532715633827387360528201919388346974995526450519367720231183334854549988196237004475722495824750461240932311816208592150378893834648925853238338569946927779783290912768.0000      
0.1330
    126    128   87.1    0.1330 
681132285274491484161243215985802083203015527781088001337043061950781182144976895679399310850408377511625546653381486739000742658041705064944044916915508066394096693647208512677645327142967564884415698417795030949051592461843703368337509482027434783865186831385716495256830620556539297395007180242944.0000      
0.1330
    127    129   90.0    0.1330 
8586361285274867977317983627880675195888367205266946823875086758576396499859405467000972306536804015885585025498257525901661362953106035517447765413709082835311404274460811711724690581122450712229446893704654766117591429249706475246937927408532911949332388774840804888127615656065912747528657557258240.0000      
0.1330
    128    130   90.0    0.1330 
10416499455887156190636893368862717330532413557481396728625560052022244432652121580316390468310209208180717189531087200608223608275533994357525588689616900052137547317168450210886356961535457771048029857361046090492696007708462695335019876261666436284148570421130557162231647899438301382414863481962496.0000      
0.1330
    129    130   89.9    0.1330 
2413063928179385616367816155966651845639687431770941377367218530743253217399890635993519343526103783792584447978515311457375927669823027971143299280478884591288505902979428695090977142310052139491011161843592039121438142384617771934012432384519689646231794197652683289444936828043622475813368790777856.0000      
0.1330
    130    131   89.9    0.1000 
731038435152268801980275743496444853187894387751687251409052299776537334558497298152683339739717254932902781633786030283256551840640858828337961055753258392252230929034743700183903379040455724737639122288003559318021849153583578634858600938005571121984537125078039474461942314076855684672347822882816.0000      
0.1000
    134    135   92.9    0.1000 
9349689720181024028833346756661438910874805841265832537584788515216883037624599176630001249855040169698596008376659015875712508916183808742474577695011711047683179151207691992153016509097048105067747558968900793171645703486214969369748725053866359764258315260318519809494233342776038206738510976647168.0000      
0.1000
    134    136   91.0    0.1470 
21578995395875634619346950176854065729310624460502079587003225035547179365056215959849261331976575378550690418378415076124099589693081341124198592462604284380551908572801508440908510604532303892881284596618210209039930595646055409472620844300444746677552397645965775741073643376862648998613084541026304.0000      
0.1470
    136    137   91.3    0.1530 
18345794273141985199900632783452167553029108673634825493854238553845807407015412879346470044399232084157140923155881289510416760951941825720055945100293241584393578473196150369288738056366528851798785649339873131909581156725276216894960265543692178512705154561907447242925113457660824242540407498473472.0000      
0.1530
    136    141   92.5    0.1530 
15960747827309009334958417219895832408755778669405475585937629813327106612476570965588241713891434137966861954011328497053308675820678009988776645757994320482573828392670037261397185703286920999423027519106131127807158893308132513006707172085328820345738610191701269649005320983422593488173094500564992.0000      
0.1530
    137    138   90.1    0.1530 
16885741950359976184428548930862799945099781302782025358918039537044361995877113441473885450477760411920761983600732421339952451391330254581966682228043505445493842742904481845211476327056447752842905318876063162598686559135371005813423932960563528277624301280487159268982652586930107490856674076393472.0000      
0.1530
    138    139   91.1    0.1830 
4534891767210825598911117232452622353859698140240595814528178617361587184532876139518315572582304752860381102471504781456134657889551255210208156307006242001196202377366614995463843403467075506852853517311670278446057579872247398132492844769789827801791660912284906947051824870607598602686610622382080.0000      
0.1830
    139    140   90.0    0.1780 
6489121387404919369259885816610774243910210293290741990813276768088290978540475441129643868135007148608766761399300879129713930112796649028505671170397765430252340117309769435632248330310847591827430412967925816859211347165789049570853606833188788069719161282731201820722022509341871861923358695227392.0000      
0.1780
    141    142   96.4    0.1250 
3264325785592613916656838020662842954132616417553682753881755483054175654879705225124467257659876963743096254362199335521519234073882214727771164280525431764645011945829391754816256363213750805430614092661668513503458955709624749250162281385424781466814737841369752575428482178625882672312280525307904.0000      
0.1250
    141    143   95.1    0.1250 
4916934345578519879834554698213963441186173278067951432739756738974922491164530265882210155029461698005956391278825048986460899441070232199590837308276913582380268336101533817823670508332559719965835636257115302288970028227786126632097095170404606521683504925172756370034918701172488954794650506362880.0000      
0.1250
step 0
Warning: 1-4 interaction between 8 and 11 at distance 
69008427917244066964689636340316570880265369719627872869604022583291580491231208238443838714888354419395116173712087161675917556393416391272692130161442715154655952825595351038111267358749249939088529435189771182821067835386026050052090870105634853684238393566438589711147635959297347833963706153172992.000 
which is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

-------------------------------------------------------
Program mdrungromacs_mpi, VERSION 3.3.3
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 96 ]

-------------------------------------------------------

I go back to my structure and again I minimize it but this error come again. 
It is my surprise why  dos'nt It occure when I do mdrun in non parallel 
mode.
I do mdrun as parallel also for Energy minimization, but the error come that 
my structure should be minimize.  
Even I do this process for the file in gromacs tutorial, again this promlem 
appeares, 
any help appriciated.
Thanks


--
Tehran University of Medical Sciences
www.tums.ac.ir


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