It is a metal-water complex. At that time, I thought it was convenient to use MOLECULE keyword. now I saw the restart doesnot work (even only with the velocity and position). I just tried with INTERMOLECULAR. The restart works! why? and why not for all? Because I was lazy. <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;"> <div class="im">I see in your coord section you specify a molname for only few atoms: why? and why not for all? </div><div class="im">Liu wrote: > 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. > > 2009/12/10 Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> </div><div class="im">> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>> > </div><div class="im">> 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 > > 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 > > > > 2009/12/10 Liu <<a href="mailto:xiand...@gmail.com">xiand...@gmail.com</a> </div>> <mailto:<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">> <mailto:<a href="mailto:xiand...@gmail.com">xiand...@gmail.com</a>>>> > > > > 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> > <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> > > <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> > <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>>> > > > > 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> <mailto:<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">> <mailto:<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> > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a>> > > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a> </div>> <mailto:<a href="mailto:cp2k%25252B...@googlegroups.com">cp2k%252Bu...@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> <mailto:<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">> <mailto:<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> > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a>> > > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@googlegroups.com</a> </div>> <mailto:<a href="mailto:cp2k%25252B...@googlegroups.com">cp2k%252Bu...@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> > <mailto:<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> > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@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> > <mailto:<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> > <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com">cp2k%2Bun...@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>. -- 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>