<span dir="ltr" style="white-space: pre-wrap;">Greetings,
I have recently started using cp2k and I'm a beginner.
I'm writing to you because I need help with a molecular dynamics calculation.
My system consists of a silver surface that interacts with an aqueous solution.
I applied the PBCs only along the X and Y axes, but not along Z (in that Z direction I have the solution that interacts with the surface).
The silver surface is parallel to the XY plane
I set in the & POISSON section:
<br></span><div><span dir="ltr" style="white-space: pre-wrap;">POISSON_SOLVER ANALYTIC
Unfortunately, however, it happens that the bonds of some water molecules tend to break when they reach the edge of the simulation box along Z, as if the atoms interacted with the image of my surface, which is located along Z.
I tried to change the algorithm to POISSON_SOLVER but got the same results.
At this point, with the VMD software I entered the size of the simulation box that I entered in the Cp2k input and I visualized the system image along z.
I observed (as you can see in the following image) that the hydrogen atoms tend to collapse towards the silver atoms of the image along z (this however should not happen because in PERIODIC I have set only the X and Y axes).
These are the dimensions of the simulation box:</span><br></div><div><span dir="ltr" style="white-space: pre-wrap;"><br></span></div><div><span dir="ltr" style=""><span style="white-space: pre-wrap;">&CELL
ABC 16.36 16.36 16.78
PERIODIC XY
&END CELL</span></span></div><div><span dir="ltr" style=""><span style="white-space: pre-wrap;"><br></span></span></div><div><span dir="ltr" style=""><span style="white-space: pre-wrap;">In the following images, however, we can see how the atoms that are subject to breaking of the bonds are "attracted" by atoms of the image surface along z (which should not exist, however).</span><span style="white-space: pre-wrap;"><br></span></span></div><div><span dir="ltr" style=""><br></span></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;">In the following image there is the initial situation:</span><br></span></div><div><span dir="ltr" style=""><img alt="01.png" data-iml="126105487.70000005" width="534px" height="321px" src="cid:e52f9953-f2b1-4c0e-a603-743dbe77ad39"><br></span></div><div><span dir="ltr" style=""><br></span></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;">The following image shows the breaking of some chemical bonds: (</span></span><span style="white-space: pre-wrap;">this occurs after a few thousand of molecular dynamics steps)</span></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;"><img alt="02.png" data-iml="126202790.0999999" width="534px" height="351px" src="cid:24d5677a-1ec3-4892-98d3-af4b9a6d8ccb"><br></span></span></div><div><br></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;"><span dir="ltr">Finally, in this image I show the image of the system along Z, and it is evident that the hydrogen atoms converge towards a silver atom in the image:</span>
<img alt="03.png" data-iml="126344477.20000005" width="534px" height="431px" src="cid:85dcffd1-ebb3-4352-b31b-8ddc20121fe7">
</span></span></div><div><br></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;"><span dir="ltr">Here is my input: (I apologize for any mistakes but I am learning and I may have made many mistakes)</span></span></span></div><div><span dir="ltr" style=""><span dir="ltr" style="white-space: pre-wrap;"><br></span></span></div><div><span dir="ltr" style=""><span dir="ltr" style=""><div style=""><span style="white-space: pre-wrap;">&FORCE_EVAL</span></div><div style=""><span style="white-space: pre-wrap;"> METHOD QUICKSTEP</span></div><div style=""><span style="white-space: pre-wrap;"> &DFT</span></div><div style=""><span style="white-space: pre-wrap;"> &QS</span></div><div style=""><span style="white-space: pre-wrap;"> METHOD xTB</span></div><div style=""><span style="white-space: pre-wrap;"> &xTB</span></div><div style=""><span style="white-space: pre-wrap;"> &PARAMETER</span></div><div style=""><span style="white-space: pre-wrap;"> DISPERSION_PARAMETER_FILE dftd3.dat</span></div><div style=""><span style="white-space: pre-wrap;"> &END PARAMETER</span></div><div style=""><span style="white-space: pre-wrap;"> DO_EWALD T</span></div><div style=""><span style="white-space: pre-wrap;"> CHECK_ATOMIC_CHARGES F</span></div><div style=""><span style="white-space: pre-wrap;"> STO_NG 6</span></div><div style=""><span style="white-space: pre-wrap;"> &END xTB</span></div><div style=""><span style="white-space: pre-wrap;"> &END QS</span></div><div style=""><span style="white-space: pre-wrap;"> &POISSON</span></div><div style=""><span style="white-space: pre-wrap;"> PERIODIC XY</span></div><div style=""><span style="white-space: pre-wrap;"> POISSON_SOLVER IMPLICIT</span></div><div style=""><span style="white-space: pre-wrap;"> &EWALD</span></div><div style=""><span style="white-space: pre-wrap;"> EWALD_TYPE SPME</span></div><div style=""><span style="white-space: pre-wrap;"> &END EWALD</span></div><div style=""><span style="white-space: pre-wrap;"> &END POISSON</span></div><div style=""><span style="white-space: pre-wrap;"> &SCF</span></div><div style=""><span style="white-space: pre-wrap;"> SCF_GUESS ATOMIC</span></div><div style=""><span style="white-space: pre-wrap;"> MAX_SCF 250</span></div><div style=""><span style="white-space: pre-wrap;"> EPS_SCF 1.e-6</span></div><div style=""><span style="white-space: pre-wrap;"> &OT</span></div><div style=""><span style="white-space: pre-wrap;"> MINIMIZER CG</span></div><div style=""><span style="white-space: pre-wrap;"> PRECONDITIONER FULL_ALL</span></div><div style=""><span style="white-space: pre-wrap;"> ENERGY_GAP 0.01</span></div><div style=""><span style="white-space: pre-wrap;"> &END</span></div><div style=""><span style="white-space: pre-wrap;"> &OUTER_SCF</span></div><div style=""><span style="white-space: pre-wrap;"> EPS_SCF 1.e-6</span></div><div style=""><span style="white-space: pre-wrap;"> MAX_SCF 250</span></div><div style=""><span style="white-space: pre-wrap;"> &END</span></div><div style=""><span style="white-space: pre-wrap;"> &END SCF</span></div><div style=""><span style="white-space: pre-wrap;"> &END DFT</span></div><div style=""><span style="white-space: pre-wrap;"> &SUBSYS</span></div><div style=""><span style="white-space: pre-wrap;"> &CELL</span></div><div style=""><span style="white-space: pre-wrap;"> ABC 16.36 16.36 16.78 </span></div><div style=""><span style="white-space: pre-wrap;"> PERIODIC XY</span></div><div style=""><span style="white-space: pre-wrap;"> &END CELL</span></div><div style=""><span style="white-space: pre-wrap;"> &COORD</span></div><div style=""><span style="white-space: pre-wrap;">Ag 1.4315000000000003E+01 2.0449999999999999E+00 0.0000000000000000E+00</span></div><div style=""><span style="white-space: pre-wrap;">Ag 1.4315000000000003E+01 0.0000000000000000E+00 2.0449999999999999E+00</span></div><div style=""><span style="white-space: pre-wrap;">Ag 1.2270000000000000E+01 0.0000000000000000E+00 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style=""><span style="white-space: pre-wrap;">H 1.1228282480184104E+01 5.8992226772976357E+00 1.3704389902691176E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.2093495187719654E+01 6.3802223019628785E+00 1.3951361981571450E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2372239085197700E+01 6.6620772802136932E+00 1.3017723024421215E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 7.6072628736862198E+00 1.4143232286731326E+01 1.3198007373404922E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 6.7909145599166552E+00 1.3539129410428993E+01 1.3289103467802672E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 6.0242256517376216E+00 1.4199248955115085E+01 1.3143675818563020E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0974552774549002E+01 1.4328691391764202E+01 1.1610871437220414E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 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8.8945655430272499E+00 9.6108776625002879E+00 1.3890450301473663E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 9.5090719972450799E+00 8.9227009007078166E+00 1.3464835968899083E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 9.0596685368937653E+00 1.3480797405054171E+01 1.5091150758091876E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 9.8789522191634518E+00 1.3397850226205906E+01 1.5699692621537427E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0417678658528025E+01 1.2742786656088144E+01 1.5123242885329629E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0121805117117521E+01 8.0167385314120363E+00 9.5472588364735511E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.0931393632054810E+01 8.5278713542123139E+00 9.1976917869625421E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.1457129560653859E+01 8.5509342483880992E+00 1.0074880939843327E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 4.4530148432660557E+00 1.5937293497748151E+01 1.3559784956077765E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 4.8067462210074048E+00 1.5760448989341985E+01 1.4495067818889769E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 5.4958579816188946E+00 1.6523357553128619E+01 1.4587358967930788E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.6243885823087844E+01 8.8717655563448936E+00 1.0523599139069795E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.5457047796812317E+01 9.1785298306708327E+00 9.9401225490329654E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.4809337329485567E+01 9.3707415105841410E+00 1.0704732691846674E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 7.9661510997408891E-01 4.3773427987910711E+00 9.4629111439899134E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.6436509957757610E+00 4.0942238673928921E+00 8.9741663337980775E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 2.2930348873580817E+00 4.6888775167748946E+00 9.5020252055895291E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.3183531937623528E+01 9.5131942067713613E+00 9.1271898176361574E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.3149463748202699E+01 1.0381086405440330E+01 8.5911176442091968E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2543513849095907E+01 1.0921920925318432E+01 9.2007095882929164E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2162678579194713E+01 1.5794073182145654E+01 9.1789262290251745E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.1840890394062809E+01 1.4918977062239364E+01 8.7655653900651735E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0883635179343804E+01 1.4979074921619604E+01 9.1085324530542522E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 7.7594449510107841E+00 1.6387578447975066E+01 1.3503963548594026E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 8.3554837399856066E+00 1.6769298581739079E+01 1.4240356243336137E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 8.7185246808441033E+00 1.7570056813515325E+01 1.3719973773075733E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 9.1946774994007352E-01 1.4257911264440768E+01 1.1110065684189474E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.1119698356209684E+00 1.5064343941366049E+01 1.0523703147267394E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.8732718979447678E+00 1.5475425662405266E+01 1.1057291839875262E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.6620375906985321E+00 1.4031690162169635E+01 1.4036879950722744E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.1463233046508594E+00 1.3271484731406877E+01 1.4473085128526177E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 2.7202676858894437E-01 1.3359815117598238E+01 1.3955279432685499E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 9.0900554778134328E+00 1.4774713269925615E+01 8.7740096095609275E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 9.0841076204292399E+00 1.3782605843039011E+01 8.5615505590147301E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 8.6325013302621780E+00 1.3373141909038631E+01 9.3773088063033860E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 9.3352900737754201E+00 4.6649099715469440E+00 9.2160573708371381E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 9.8422694472223320E+00 5.1657640191980070E+00 8.4920224096670687E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0271301004734129E+01 5.9031534533033989E+00 9.0512372752631940E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.1168470261784023E+01 1.1539970657550519E+01 8.9293600204422034E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.1366320330491366E+01 1.2504898179278223E+01 8.6766814039122515E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.0898612934696848E+01 1.2933615600868501E+01 9.4745790142430231E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.4196880053359250E+01 9.0881397662253693E+00 1.4583551212793159E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.3411436663574165E+01 8.5541062138736876E+00 1.4951070012622981E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2679159979038538E+01 9.2623465194842733E+00 1.4894816831716074E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2668363460340291E+01 1.8427803167493750E+00 1.0527576643438991E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.3372355027400440E+01 1.2374787112429926E+00 1.0101488761345378E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.3572107253811110E+01 6.9233124940455282E-01 1.0940490377404425E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 5.1444960172647853E+00 1.0707351163561595E+01 9.9239900082341403E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 4.8470442566945939E+00 1.1060672054714157E+01 9.0099907249200033E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 3.8742448053587335E+00 1.1246155099323110E+01 9.2679826383142139E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.1359681136803070E+01 1.4483316080393537E+01 1.4040814099325791E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.2146684346534171E+01 1.5132903875977728E+01 1.3960514790994377E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.2164656568601139E+01 1.5348594060017769E+01 1.2968857278528429E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.4279730864098395E+01 5.0093730736608357E+00 9.0823116602575773E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 1.3523515043812409E+01 4.4975484448310619E+00 8.6353788462984156E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.3519506410075280E+01 3.6798005409044512E+00 9.2415158472816259E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 1.7398913817627157E+00 4.7947646780744639E+00 1.3499274711809578E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 7.4843574393379997E-01 4.5972640875183233E+00 1.3381967710160596E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 7.8063506195760146E-01 3.8260047515146933E+00 1.2730406085580629E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 4.3601712699507473E+00 5.1000781397860466E+00 1.2258913534913582E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 4.7480663716290916E+00 6.0179138390533344E+00 1.2023282216713586E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 4.1303559809927455E+00 6.6166953778476527E+00 1.2576498268654630E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 5.5491865924931325E+00 5.0857518437164799E+00 1.4830996793528554E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 6.4722436575147402E+00 5.3874865761271824E+00 1.4509649200785335E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 6.4133333699033912E+00 5.0851010776979173E+00 1.3543315371372451E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.8373234805894856E+00 1.0759900055173981E+01 1.2020441837222492E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 1.4672223230327985E+00 1.1509785838563884E+01 1.1437029796595452E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.9571773542858768E+00 1.1364147150466755E+01 1.0557143639945940E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 1.3548159349007327E+00 6.5146018976766848E+00 8.9895027623555759E+00</span></div><div style=""><span style="white-space: pre-wrap;">O 3.7403870674632939E-01 6.6823363893228098E+00 8.7743942729299942E+00</span></div><div style=""><span style="white-space: pre-wrap;">H -3.5946164548139974E-02 5.8034469424041015E+00 9.0819048112506042E+00</span></div><div style=""><span style="white-space: pre-wrap;">H 7.1107871694885096E+00 2.9957850379400530E+00 1.0395663198744657E+01</span></div><div style=""><span style="white-space: pre-wrap;">O 7.8077085593728670E+00 2.3093730464430262E+00 1.0101639784280273E+01</span></div><div style=""><span style="white-space: pre-wrap;">H 7.9043192449986526E+00 1.7695235559647979E+00 1.0966605596579099E+01</span></div><div style=""><span style="white-space: pre-wrap;"> &END COORD</span></div><div style=""><span style="white-space: pre-wrap;"> &END SUBSYS</span></div><div style=""><span style="white-space: pre-wrap;">&END FORCE_EVAL</span></div><div style=""><span style="white-space: pre-wrap;">&MOTION</span></div><div style=""><span style="white-space: pre-wrap;"> &CONSTRAINT</span></div><div style=""><span style="white-space: pre-wrap;"> &FIXED_ATOMS</span></div><div style=""><span style="white-space: pre-wrap;"> COMPONENTS_TO_FIX XYZ</span></div><div style=""><span style="white-space: pre-wrap;"> LIST 1..128</span></div><div style=""><span style="white-space: pre-wrap;"> &END FIXED_ATOMS</span></div><div style=""><span style="white-space: pre-wrap;"> &END CONSTRAINT</span></div><div style=""><span style="white-space: pre-wrap;"> &MD</span></div><div style=""><span style="white-space: pre-wrap;"> ENSEMBLE NVE</span></div><div style=""><span style="white-space: pre-wrap;"> STEPS 10000</span></div><div style=""><span style="white-space: pre-wrap;"> TIMESTEP 0.1</span></div><div style=""><span style="white-space: pre-wrap;"> TEMPERATURE 300.0</span></div><div style=""><span style="white-space: pre-wrap;"> TEMP_TOL 50.0</span></div><div style=""><span style="white-space: pre-wrap;"> &END MD</span></div><div style=""><span style="white-space: pre-wrap;">&END MOTION </span></div><div style=""><span style="white-space: pre-wrap;">&GLOBAL</span></div><div style=""><span style="white-space: pre-wrap;"> PROJECT testAg_surf</span></div><div style=""><span style="white-space: pre-wrap;"> RUN_TYPE MD </span></div><div style=""><span style="white-space: pre-wrap;"> PRINT_LEVEL LOW</span></div><div style=""><span style="white-space: pre-wrap;">&END GLOBAL</span></div><div style=""><span style="white-space: pre-wrap;"><br></span></div><div style=""><span style="white-space: pre-wrap;"><br></span></div><div style=""><span style="white-space: pre-wrap;"><br></span></div><div style=""><span style="white-space: pre-wrap;"><br></span></div><div style=""><br><span style="white-space: pre-wrap;">Thank you very much for your help.</span> <span style="white-space: pre-wrap;"><br></span></div>
</span></span></div>
<p></p>
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