1) is ruled out. the restraint was there, so the geometry didnot explode. 2).INTERMOLECULER Maybe I should have used this keyword ? So no connectivity was needed any longer . Am I right ? Liu <div class="gmail_quote">2009/12/10 Liu <<a href="mailto:xiand...@gmail.com">xiand...@gmail.com</a>> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Hi Teo, the input is as follows, &FORCE_EVAL METHOD Quickstep &DFT POTENTIAL_FILE_NAME GTH_POTENTIALS BASIS_SET_FILE_NAME GTH_BASIS_SETS CHARGE 2 &MGRID CUTOFF 320 &END MGRID &QS EPS_DEFAULT 1.0E-12 &END QS &SCF &OT T MINIMIZER DIIS &END OT EPS_SCF 1.0E-6 SCF_GUESS RESTART MAX_SCF 110 &END SCF &XC &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &END XC &END DFT &SUBSYS &CELL ABC 10.50 10.50 10.50 ALPHA_BETA_GAMMA 90.0000 90.0000 90.0000 &END CELL<div class="im"> &COLVAR &DISTANCE ATOMS 13 1 &END DISTANCE &END COLVAR </div> &COLVAR &ANGLE ATOMS 13 1 14 &END ANGLE &END COLVAR &COLVAR &ANGLE ATOMS 13 1 19 &END ANGLE &END COLVAR &COORD O 4.945624262365 5.235220805899 8.003244927409 mol O 4.007891695360 3.552175895176 5.977360545441 mol O 2.285433270467 5.417764639023 6.897323134184 mol O 5.936765184537 5.829000559392 5.593775858772 mol O 4.183440185942 7.470635689797 6.674994934445 mol O 3.439793446681 5.742570923209 4.488746955268 mol H 1.793348652560 4.673685333363 6.448632172866 mol H 1.975552174635 5.586491381857 7.823579691797 mol H 6.341196051434 6.210453911837 4.735768436262 mol H 6.691670293500 5.986498079468 6.262057248960 mol H 3.355172624465 7.888242164427 6.980928704617 mol H 4.800145134415 8.144564641311 6.279932035506 mol H1 5.024438896426 4.333073695541 8.420372999423 mol H 5.417966958607 5.879810696856 8.656369353769 mol H 4.044612590192 5.703785764108 3.692496314811 mol H 2.635152794031 6.238242225502 4.179846355098 mol H 4.789074411431 2.978145753930 6.248397019420 mol H 3.308516986446 3.025660313636 5.420256518302 mol Al 4.199165250044 5.577278113875 6.261316460312 mol O 1.929962666627 2.386347797671 4.459074121571 O 1.952979070957 0.358546555482 9.269519490418 O 0.026958456120 2.197269503272 8.735038598236 O -1.362279675283 6.955540825025 1.744054996031 O -2.899500082333 1.789177922013 2.425421734762 O -2.274297024247 5.797133615346 7.045592606844 O 1.445305003994 7.051219378572 3.715192156899 O 0.940001451447 4.990446887363 9.698689854397 O 0.031348798328 11.381839465447 1.904616048439 O -3.581560970691 9.411668100190 12.775652442937 O -1.647961298578 9.922630983793 8.321980647542 O 0.106325557834 -1.237262561258 0.213551451909 O 4.599334494386 0.610540436556 2.704211560407 O 6.110865497086 2.836144155293 9.037244996699 O 8.444963101791 12.757951977677 5.545652221781 O 4.717343810939 5.987976596723 1.780097066543 O 6.784715588065 6.889213503169 3.276373325092 O 0.383247580198 14.072985902428 6.230493216461 O 3.234318655214 3.857825154773 0.818868910110 O 1.963164530700 8.951099554455 7.068571426781 O 6.144029555568 6.796223574397 9.580179213359 O 8.048882212076 9.883185225311 4.810587174940 O 2.473675663501 10.303668237070 4.613284200787 O 3.999780862821 1.198425534797 0.139239985704 O 5.918103249911 1.825332131822 6.347934161668 O 5.870936669144 -0.907093857702 6.224645660032 O 8.497631912579 3.194191743002 -0.218198563998 O 10.562268276538 4.605445613458 2.706189110743 O 9.937102032317 8.200210165838 6.102555829864 O 8.599241385563 5.812668445953 9.929894326533 O 2.711405118216 8.000171931520 11.614265439006 O 6.448641165374 9.853545022641 10.091854412172 H 2.094505467531 1.370769732124 4.450185540604 H 1.766899467254 2.576096119515 3.490475988652 H 1.282647036726 -0.136316253288 9.811359473370 H 2.655785237669 0.719499451687 9.879362070408 H -0.608993486319 2.410722591791 9.424195138941 H 0.567781798217 1.367820187953 8.901435796804 H -0.746695201051 7.579922756681 1.272004746797 H -0.756268349803 6.209154398982 2.121980920129 H -2.895078695179 0.880540905683 2.018484814746 H -3.812114079147 1.945095390040 2.723542853332 H -1.450477955480 5.414594613020 6.547688311675 H -2.100265303911 5.762411444564 7.988207299506 H 0.856199581228 7.443072324347 4.447509731648 H 1.683787441702 7.732202944333 3.062648462236 H 0.914577100384 3.982820700161 9.483944679985 H -0.013545868383 5.297204143626 9.652724302908 H 0.842855940551 11.867508142867 1.624433490893 H -0.554679549011 12.094267611684 2.329428790545 H -3.648772260742 9.475561082667 11.749156370492 H -3.946707998081 8.505718208125 13.033750646306 H -1.349673886536 10.831974112009 7.968158045454 H -1.467941976087 9.098874977651 7.662349937164 H -0.157891145685 -0.548152766129 0.913773510052 H -0.486176442427 -1.036451242486 -0.545737942048 H 5.285066261429 -0.057476231123 2.694625810112 H 4.079966836623 0.551927307125 3.573612525248 H 6.015753238192 2.297712230229 8.175869506495 H 5.470262328903 2.382741162434 9.713210640781 H 9.282217259184 13.252061003334 5.800368726315 H 8.310801713089 13.069470210375 4.633682212258 H 4.392983089723 5.075736957232 1.274546475430 H 3.981000248919 6.671489138137 1.565186021664 H 7.666107418592 6.715687507639 2.810668805098 H 6.049329065526 6.466893192597 2.736263305956 H 0.792787273346 13.490990322042 5.543123131905 H 0.418620204652 13.482889458348 7.083779005514 H 2.540452439292 4.509285556271 0.546998335709 H 3.399993082999 3.414505470904 -0.002840227708 H 1.032218251313 8.673654190202 7.041983379026 H 2.094522687566 9.533513585930 7.911335251137 H 5.836279591854 6.578895551319 10.522628960955 H 7.128416505935 6.551955664875 9.651665340638 H 8.334130619874 10.823573762782 5.138777207840 H 7.835191538334 10.053541130268 3.845182999807 H 2.002893030136 9.680973570920 4.067457026619 H 2.302316195807 10.008164610561 5.548627414794 H 4.271980573949 1.089340786239 1.114383694195 H 4.742087428870 0.658613977652 -0.337748849214 H 5.834805046820 0.889378508637 6.043605489317 H 6.885651604423 2.000027177721 6.057665925746 H 6.514304273259 -0.920000002808 6.971136480943 H 6.480216340233 -0.978037422098 5.424181543392 H 7.718541069821 3.011662500946 -0.863906539993 H 8.130716210257 2.931264814758 0.649970337419 H 11.396873489626 5.053367889582 2.899398079628 H 10.639341197546 4.446886981342 1.681298091029 H 9.275748751503 8.741134402620 5.594644857244 H 9.508184542015 7.278563165823 6.211855784019 H 8.456691240675 4.796394786938 10.089977970213 H 8.591160601702 6.196940377323 10.904893066768 H 1.850384315640 7.951775925152 11.140192575907 H 2.859191674027 8.984887322643 11.845765015442 H 6.092174319778 8.925042319655 9.772217739704 H 7.222986151208 9.962961083214 9.512548867753 &END COORD &KIND H BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q1 &END KIND &KIND H1 BASIS_SET NONE POTENTIAL GTH-BLYP-q1 GHOST &END KIND &KIND O BASIS_SET TZV2P-GTH POTENTIAL GTH-BLYP-q6 &END KIND &KIND Al BASIS_SET DZVP-GTH POTENTIAL GTH-BLYP-q3 &END KIND &END SUBSYS &END FORCE_EVAL &GLOBAL PROJECT A RUN_TYPE MD PRINT_LEVEL MEDIUM &PRINT &EACH &END EACH &END PRINT &END GLOBAL &MOTION<div class="im"> &CONSTRAINT &COLLECTIVE TARGET 1.89 MOLECULE 1 COLVAR 1 &RESTRAINT k 0.1 &END RESTRAINT &END COLLECTIVE </div> &COLLECTIVE TARGET 1.869 <div class="im"> MOLECULE 1 COLVAR 2 &RESTRAINT k 0.1 &END RESTRAINT &END COLLECTIVE </div> &COLLECTIVE TARGET 2.1457 <div class="im"> MOLECULE 1 COLVAR 3 &RESTRAINT k 0.1 &END RESTRAINT &END COLLECTIVE &END CONSTRAINT </div> &MD ENSEMBLE NVT STEPS 50000 TIMESTEP 0.5 TEMPERATURE 330.0 &THERMOSTAT &NOSE LENGTH 3 YOSHIDA 3 TIMECON 1000.0 MTS 2 &END NOSE &END THERMOSTAT &END MD &PRINT &TRAJECTORY &EACH MD 20 &END EACH &END TRAJECTORY &END PRINT &END MOTION could you please give some further comment on this ? Thanks for your help Liu <div class="gmail_quote">2009/12/10 Teodoro Laino <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>><div> <div></div><div class="h5"> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Basically this issue has many different sources. The two most important: -) The first problem is that you should seriously think if you want help: in this case next time I would recommend to send the entire input file and not just pieces of it. -) The second problem is that CP2K has not a manual: it is difficult to learn but we do provide (for extremely motivated people) quite a big number of working input files, which cover most of its functionalities. It would be ideal that before mixing keywords and subsections you would train yourself trying first to understand (on your own) what is the logic of the code. Having said that, based on the minimal amount of information you sent us, I can try to guess: 1) probably you ask cp2k to build the topology. At the beginning the geometry is reasonable and cp2k is able to build a correct connectivity. When you restart (connectivity is not restartable!) cp2k builds a new connectivity and very probably your input file is so well tuned that the system just explodes -> new connectivity is a mess -> the intramolecular constraint cannot be applied (your restratins is intramolecular!!) 2) with the restraint setup below (the only piece you have sent) you are specifying the same restraint for all molecular types 1. if you want to apply just 1 restraint (between two atoms not belonging to the same molecule) there is a keyword to be specified: <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#desc_INTERMOLECULAR" target="_blank">http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#desc_INTERMOLECULAR</a> 3) if you really want to have the same restraint appled to all molecular types 1 then I would recommend you to have a topology file. This will guarantee that even if you are trying to simulate the "big bang" the specification of molecular connectivity will not depend on how far are the atoms. 4) if you don't need the connectivity (because your goal is to model some explosion [for example..]) then just disable the generation of the connectivity. Since the possible sources are many (because mainly we cannot understand what you really want to do!) I would suggest you : take your time, think what you want to do with cp2k and your present run. Teo <div><div></div><div> Liu wrote: > Hi all, > > I used the following COLVAR and CONSTRAINT to do a MD run and it goes > well. > > &COLVAR > &DISTANCE > ATOMS 13 1 > &END DISTANCE > &END COLVAR > > &CONSTRAINT > &COLLECTIVE > TARGET 1.89 > MOLECULE 1 > COLVAR 1 > &RESTRAINT > k 0.1 > &END RESTRAINT > &END COLLECTIVE > > &END CONSTRAINT > > When I added this: > &EXT_RESTART > RESTART_FILE_NAME A-1.restart > RESTART_DEFAULT TRUE > &END EXT_RESTART > > the error happened: > > | Error in constraints setup! > | A constraint has been defined for a molecule type > | but the atoms specified in the constraint and the a | > Error in constraints setup! > | A constraint has been defined for a molecule type > | but the atoms specified in the constraint and the atoms > defined for > | the molecule DO NOT match! > > Any suggestion is appreciated ! > > cheers, > Liu > > -- > > You received this message because you are subscribed to the Google Groups "cp2k" group. > To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>. > To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>. > For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. > > > -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. </div></div></blockquote></div></div></div> </blockquote></div>