Hi Teo, What I want to do is to restrain the 3 colvars to the respective target values. So the connectivity does not matter. Liu. <div class="gmail_quote">2009/12/10 Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@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;">It is not a matter of using a specific keyword. It is a matter of understanding what you are doing. If you specify INTERMOLECULAR the topology will still be built: you may not get that error but the problem is still there. I see in your coord section you specify a molname for only few atoms: why? and why not for all? do you wish to have a connectivity built or not? do you want to specify a restraint for intermolecular or intramolecular ? in short words: what do you want to do? Teo <div class="im"> Liu wrote: > > 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>> 2009/12/10 Liu <<a href="mailto:xiand...@gmail.com">xiand...@gmail.com</a> <mailto:<a href="mailto:xiand...@gmail.com">xiand...@gmail.com</a>>> <div><div></div><div class="h5">> > 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 > > &COLVAR > &DISTANCE > ATOMS 13 1 > &END DISTANCE > &END COLVAR > &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 > > &CONSTRAINT > &COLLECTIVE > TARGET 1.89 > MOLECULE 1 > COLVAR 1 > &RESTRAINT > k 0.1 > &END RESTRAINT > &END COLLECTIVE > &COLLECTIVE > TARGET 1.869 > MOLECULE 1 > COLVAR 2 > &RESTRAINT > k 0.1 > &END RESTRAINT > &END COLLECTIVE > &COLLECTIVE > TARGET 2.1457 > MOLECULE 1 > COLVAR 3 > &RESTRAINT > k 0.1 > &END RESTRAINT > &END COLLECTIVE > &END CONSTRAINT > &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 > > 2009/12/10 Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> </div></div>> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>> <div><div></div><div class="h5">> > 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 > > > 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">cp...@googlegroups.com</a> </div></div>> <mailto:<a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>>. <div class="im">> > To unsubscribe from this group, send email to > <a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a> </div>> <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a>>. <div class="im">> > 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">cp...@googlegroups.com</a> </div>> <mailto:<a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>>. <div class="im">> To unsubscribe from this group, send email to > <a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a> </div>> <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a>>. <div><div></div><div class="h5">> 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">cp...@googlegroups.com</a>. > To unsubscribe from this group, send email to > <a href="mailto:cp2k%2Bun...@googlegroups.com">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">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com">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>