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