<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Henrique Junior, <div class=""><br class=""></div><div class="">if these are subsequent step separated by 0.5fs than this looks all very reasonable to me. </div><div class="">The atoms don’t move a hell a lot within half a femtosecond. </div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas Kühne<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 27.04.2022 um 21:22 schrieb Henrique Junior <<a href="mailto:henriquecsj@gmail.com" class="">henriquecsj@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><p class="">Hi everyone,
I hope you are all doing fine.</p><p class="">CP2K is
completely new for me, and it is proving to be a challenge. I am attempting to simulate
liquid DMSO (a simple molecule with 10 atoms) just as a test. So far, I have tried
to build my input based on tutorials simulating liquid water and tweaking it
for DMSO.</p><p class="">The
calculation is running fine and converging quite smoothly but looking at the <a href="http://DMSO-pos-1.xyz" class="">DMSO-pos-1.xyz</a>
file that’s being generated I can see that the atoms are barely shaking. I’m
attaching (and showing below) my input and the xyz file. Any help would be much
appreciated.</p><p class="">Thanks in
advance.</p><p class="">Vvvvvvvvvvvvvvvvvvvvvvvvvv
INPUT vvvvvvvvvvvvvvvvvvvvvvvvvv</p><p class="">&GLOBAL<br class=""> PROJECT DMSO<br class=""> RUN_TYPE MD <br class="">&END GLOBAL<br class=""><br class="">&FORCE_EVAL<br class=""> METHOD Quickstep<br class=""> &DFT<br class=""> BASIS_SET_FILE_NAME GTH_BASIS_SETS<br class=""> POTENTIAL_FILE_NAME GTH_POTENTIALS <br class=""> CHARGE 0<br class=""> MULTIPLICITY 1<br class=""><br class=""> &MGRID<br class=""> CUTOFF [Ry] 400 <br class=""> &END<br class=""><br class=""> &QS<br class=""> METHOD GPW <br class=""> EPS_DEFAULT 1.0E-10 <br class=""> EXTRAPOLATION ASPC <br class=""> &END<br class=""><br class=""> &POISSON<br class=""> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver<br class=""> &END<br class=""><br class=""> &PRINT<br class=""> &E_DENSITY_CUBE OFF<br class=""> &END E_DENSITY_CUBE<br class=""> &MO_CUBES<br class=""> NLUMO 4<br class=""> NHOMO 4<br class=""> WRITE_CUBE .FALSE.<br class=""> &EACH<br class=""> MD 10<br class=""> &END<br class=""> &END<br class=""> &END<br class=""><br class=""> &SCF <br class=""> SCF_GUESS ATOMIC <br class=""> MAX_SCF 500<br class=""> EPS_SCF 1.0E-6 <br class=""> &OT<br class=""> PRECONDITIONER FULL_SINGLE_INVERSE<br class=""> MINIMIZER DIIS<br class=""> &END OT<br class=""> &OUTER_SCF ! repeat the inner SCF cycle 10 times<br class=""> MAX_SCF 10<br class=""> EPS_SCF 1.0E-6<br class=""> &END<br class=""> &PRINT<br class=""> &RESTART OFF<br class=""> &END<br class=""> &END<br class=""> &END SCF<br class=""><br class=""> &XC<br class=""> &XC_FUNCTIONAL <br class=""> &PBE<br class=""> &END<br class=""> &END XC_FUNCTIONAL<br class=""> ! adding Grimme's D3 correction (by default without C9 terms) <br class=""> &VDW_POTENTIAL<br class=""> POTENTIAL_TYPE PAIR_POTENTIAL <br class=""> &PAIR_POTENTIAL<br class=""> PARAMETER_FILE_NAME dftd3.dat<br class=""> TYPE DFTD3<br class=""> REFERENCE_FUNCTIONAL PBE<br class=""> R_CUTOFF [angstrom] 16<br class=""> &END<br class=""> &END VDW_POTENTIAL<br class=""> &END XC<br class=""> &END DFT<br class=""> <br class=""> &SUBSYS<br class=""> &CELL <br class=""> ABC [angstrom] 9.0 9.0 9.0<br class=""> &END CELL<br class=""><br class=""> &TOPOLOGY<br class=""> COORD_FILE_NAME <a href="http://DMSOcaixa.xyz" class="">DMSOcaixa.xyz</a><br class=""> COORD_FILE_FORMAT XYZ<br class=""> &END<br class=""><br class=""> &KIND H <br class=""> BASIS_SET DZVP-MOLOPT-SR-GTH <br class=""> POTENTIAL GTH-PBE-q1 <br class=""> &END KIND<br class=""> &KIND C<br class=""> BASIS_SET DZVP-MOLOPT-SR-GTH<br class=""> POTENTIAL GTH-PBE-q4<br class=""> &END KIND<br class=""> &KIND O<br class=""> BASIS_SET DZVP-MOLOPT-SR-GTH<br class=""> POTENTIAL GTH-PBE-q6<br class=""> &END KIND<br class=""> &KIND S<br class=""> BASIS_SET DZVP-MOLOPT-SR-GTH<br class=""> POTENTIAL GTH-PBE-q6<br class=""> &END KIND<br class=""> &END SUBSYS<br class="">&END FORCE_EVAL<br class=""><br class="">! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section<br class="">&MOTION<br class=""> &PRINT<br class=""> &TRAJECTORY<br class=""> &EACH<br class=""> MD 1<br class=""> &END EACH<br class=""> &END TRAJECTORY<br class=""> &VELOCITIES OFF<br class=""> &END VELOCITIES<br class=""> &FORCES OFF<br class=""> &END FORCES<br class=""> &RESTART_HISTORY<br class=""> &EACH<br class=""> MD 500<br class=""> &END EACH<br class=""> &END RESTART_HISTORY<br class=""> &RESTART<br class=""> BACKUP_COPIES 3<br class=""> &EACH<br class=""> MD 1<br class=""> &END EACH<br class=""> &END RESTART<br class=""> &END PRINT<br class=""> &GEO_OPT<br class=""> OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)<br class=""> MAX_ITER 100<br class=""> MAX_DR [bohr] 0.003 ! adjust target as needed<br class=""> &BFGS<br class=""> &END<br class=""> &END<br class=""> &MD<br class=""> ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE<br class=""> TEMPERATURE [K] 300<br class=""> TIMESTEP [fs] 0.5<br class=""> STEPS 1000<br class=""> # GLE thermostat as generated at <a href="http://epfl-cosmo.github.io/gle4md" class="">http://epfl-cosmo.github.io/gle4md</a> <br class=""> # GLE provides an effective NVT sampling.<br class=""> &THERMOSTAT<br class=""> REGION MASSIVE<br class=""> TYPE GLE<br class=""> &GLE<br class=""> NDIM 5<br class=""> A_SCALE [ps^-1] 1.00<br class=""> A_LIST 1.859575861256e+2 2.726385349840e-1 1.152610045461e+1 -3.641457826260e+1 2.317337581602e+2<br class=""> A_LIST -2.780952471206e-1 8.595159180871e-5 7.218904801765e-1 -1.984453934386e-1 4.240925758342e-1<br class=""> A_LIST -1.482580813121e+1 -7.218904801765e-1 1.359090212128e+0 5.149889628035e+0 -9.994926845099e+0<br class=""> A_LIST -1.037218912688e+1 1.984453934386e-1 -5.149889628035e+0 2.666191089117e+1 1.150771549531e+1<br class=""> A_LIST 2.180134636042e+2 -4.240925758342e-1 9.994926845099e+0 -1.150771549531e+1 3.095839456559e+2<br class=""> &END GLE<br class=""> &END THERMOSTAT<br class=""> &END<br class="">&END<br class=""></p><div class=""><br class="webkit-block-placeholder"></div>
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<span id="cid:4f895a10-994e-4a25-aebb-65d2c1ac5971"><DMSO.inp></span><span id="cid:d7f95335-f83d-48c6-8381-f228d4669b97"><<a href="http://DMSO-pos-1.xyz" class="">DMSO-pos-1.xyz</a>></span></div></blockquote></div><br class=""></div><br class=""><br class=""><div class="">
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Kühne</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Dynamics of Condensed Matter</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Chair of Theoretical Chemistry</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">University of Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Warburger Str. 100</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">D-33098 Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Germany</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class=""><a href="mailto:thomas.kuehne@upb.de" class="">thomas.kuehne@upb.de</a></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">+49/(0)5251/60-5726</div></div></div></div></div>
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