<div dir="ltr">Hi,<div><br><div>Please have a look at the setting for ab initio MD.</div><div><a href="https://brehm-research.de/files/spec_tutorial_2018.pdf">https://brehm-research.de/files/spec_tutorial_2018.pdf</a><br></div><div><br></div><div>If you want to increase the time step to 1 fs you can use deuterium mass for hydrogen atoms. </div><div><br></div><div>Best,</div><div>Dmitrii</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 26, 2022 at 5:16 AM Thomas Kühne <<a href="mailto:tkuehne@gmail.com">tkuehne@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Dear Henrique Junior, <div><br></div><div>if these are subsequent step separated by 0.5fs than this looks all very reasonable to me. </div><div>The atoms don’t move a hell a lot within half a femtosecond. </div><div><br></div><div>Best, </div><div>Thomas Kühne<br><div><br><blockquote type="cite"><div>Am 27.04.2022 um 21:22 schrieb Henrique Junior <<a href="mailto:henriquecsj@gmail.com" target="_blank">henriquecsj@gmail.com</a>>:</div><br><div><p>Hi everyone,
I hope you are all doing fine.</p><p>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>The
calculation is running fine and converging quite smoothly but looking at the <a href="http://DMSO-pos-1.xyz" target="_blank">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>Thanks in
advance.</p><p>Vvvvvvvvvvvvvvvvvvvvvvvvvv
INPUT vvvvvvvvvvvvvvvvvvvvvvvvvv</p><p>&GLOBAL<br> PROJECT DMSO<br> RUN_TYPE MD <br>&END GLOBAL<br><br>&FORCE_EVAL<br> METHOD Quickstep<br> &DFT<br> BASIS_SET_FILE_NAME GTH_BASIS_SETS<br> POTENTIAL_FILE_NAME GTH_POTENTIALS <br> CHARGE 0<br> MULTIPLICITY 1<br><br> &MGRID<br> CUTOFF [Ry] 400 <br> &END<br><br> &QS<br> METHOD GPW <br> EPS_DEFAULT 1.0E-10 <br> EXTRAPOLATION ASPC <br> &END<br><br> &POISSON<br> PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver<br> &END<br><br> &PRINT<br> &E_DENSITY_CUBE OFF<br> &END E_DENSITY_CUBE<br> &MO_CUBES<br> NLUMO 4<br> NHOMO 4<br> WRITE_CUBE .FALSE.<br> &EACH<br> MD 10<br> &END<br> &END<br> &END<br><br> &SCF <br> SCF_GUESS ATOMIC <br> MAX_SCF 500<br> EPS_SCF 1.0E-6 <br> &OT<br> PRECONDITIONER FULL_SINGLE_INVERSE<br> MINIMIZER DIIS<br> &END OT<br> &OUTER_SCF ! repeat the inner SCF cycle 10 times<br> MAX_SCF 10<br> EPS_SCF 1.0E-6<br> &END<br> &PRINT<br> &RESTART OFF<br> &END<br> &END<br> &END SCF<br><br> &XC<br> &XC_FUNCTIONAL <br> &PBE<br> &END<br> &END XC_FUNCTIONAL<br> ! adding Grimme's D3 correction (by default without C9 terms) <br> &VDW_POTENTIAL<br> POTENTIAL_TYPE PAIR_POTENTIAL <br> &PAIR_POTENTIAL<br> PARAMETER_FILE_NAME dftd3.dat<br> TYPE DFTD3<br> REFERENCE_FUNCTIONAL PBE<br> R_CUTOFF [angstrom] 16<br> &END<br> &END VDW_POTENTIAL<br> &END XC<br> &END DFT<br> <br> &SUBSYS<br> &CELL <br> ABC [angstrom] 9.0 9.0 9.0<br> &END CELL<br><br> &TOPOLOGY<br> COORD_FILE_NAME <a href="http://DMSOcaixa.xyz" target="_blank">DMSOcaixa.xyz</a><br> COORD_FILE_FORMAT XYZ<br> &END<br><br> &KIND H <br> BASIS_SET DZVP-MOLOPT-SR-GTH <br> POTENTIAL GTH-PBE-q1 <br> &END KIND<br> &KIND C<br> BASIS_SET DZVP-MOLOPT-SR-GTH<br> POTENTIAL GTH-PBE-q4<br> &END KIND<br> &KIND O<br> BASIS_SET DZVP-MOLOPT-SR-GTH<br> POTENTIAL GTH-PBE-q6<br> &END KIND<br> &KIND S<br> BASIS_SET DZVP-MOLOPT-SR-GTH<br> POTENTIAL GTH-PBE-q6<br> &END KIND<br> &END SUBSYS<br>&END FORCE_EVAL<br><br>! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section<br>&MOTION<br> &PRINT<br> &TRAJECTORY<br> &EACH<br> MD 1<br> &END EACH<br> &END TRAJECTORY<br> &VELOCITIES OFF<br> &END VELOCITIES<br> &FORCES OFF<br> &END FORCES<br> &RESTART_HISTORY<br> &EACH<br> MD 500<br> &END EACH<br> &END RESTART_HISTORY<br> &RESTART<br> BACKUP_COPIES 3<br> &EACH<br> MD 1<br> &END EACH<br> &END RESTART<br> &END PRINT<br> &GEO_OPT<br> OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)<br> MAX_ITER 100<br> MAX_DR [bohr] 0.003 ! adjust target as needed<br> &BFGS<br> &END<br> &END<br> &MD<br> ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE<br> TEMPERATURE [K] 300<br> TIMESTEP [fs] 0.5<br> STEPS 1000<br> # GLE thermostat as generated at <a href="http://epfl-cosmo.github.io/gle4md" target="_blank">http://epfl-cosmo.github.io/gle4md</a> <br> # GLE provides an effective NVT sampling.<br> &THERMOSTAT<br> REGION MASSIVE<br> TYPE GLE<br> &GLE<br> NDIM 5<br> A_SCALE [ps^-1] 1.00<br> A_LIST 1.859575861256e+2 2.726385349840e-1 1.152610045461e+1 -3.641457826260e+1 2.317337581602e+2<br> A_LIST -2.780952471206e-1 8.595159180871e-5 7.218904801765e-1 -1.984453934386e-1 4.240925758342e-1<br> A_LIST -1.482580813121e+1 -7.218904801765e-1 1.359090212128e+0 5.149889628035e+0 -9.994926845099e+0<br> A_LIST -1.037218912688e+1 1.984453934386e-1 -5.149889628035e+0 2.666191089117e+1 1.150771549531e+1<br> A_LIST 2.180134636042e+2 -4.240925758342e-1 9.994926845099e+0 -1.150771549531e+1 3.095839456559e+2<br> &END GLE<br> &END THERMOSTAT<br> &END<br>&END<br></p><div><br></div>
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<span id="gmail-m_-9134839339442403194cid:4f895a10-994e-4a25-aebb-65d2c1ac5971"><DMSO.inp></span><span id="gmail-m_-9134839339442403194cid:d7f95335-f83d-48c6-8381-f228d4669b97"><<a href="http://DMSO-pos-1.xyz" target="_blank">DMSO-pos-1.xyz</a>></span></div></blockquote></div><br></div><br><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">==============================</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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thomas D. 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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href="mailto:thomas.kuehne@upb.de" target="_blank">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-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">+49/(0)5251/60-5726</div></div></div></div></div>
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