In my opinion with small hills deposited every 100 fs, you’re unlikely to converge the Metadynamics bias. <br /><div dir="ltr"></div><div dir="ltr">You should have a look at J. Phys. Chem. B 2005, 109, 14, 6714–6721 <a href="https://doi.org/10.1021/jp045424k">https://doi.org/10.1021/jp045424k</a>,
on choosing the optimal parameters for ab initio metadynamics. However,
even with increased bias deposition rate, it is possible that meta
dynamics bias convergence could take more than hundreds or thousands of
ps depending on the system, although it’s hard to say. Maybe you can have a qualitative intepretation if you are close to convergence and do not require accurate barriers, and rather need orders of magnitude.</div><div dir="ltr">Take care :) </div><div dir="ltr">Q. </div>
<br /><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">Le dimanche 16 février 2025 à 10:19:16 UTC+1, SAURABH SINGH a écrit :<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><blockquote type="cite" style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><div dir="ltr">Thank you Quentin<br><br>My system consists of simple molecules Cl CO2 and H2O<br><br>&GLOBAL<br> PROJECT 1a<br> RUN_TYPE MD<br> PRINT_LEVEL MEDIUM<br>&END GLOBAL<br><br>#&EXT_RESTART<br> # RESTART_FILE_NAME 1a-1.restart<br>#&END EXT_RESTART<br><br>&MOTION<br> &MD<br> ENSEMBLE NVT # ENSEMBLE NVE<br> STEPS 50000<br> TIMESTEP 1<br> TEMPERATURE 300.0<br> TEMP_TOL 100<br> &THERMOSTAT<br> &NOSE<br> LENGTH 3 # 3 is the default<br> MTS 2 # 2 is the default<br> TIMECON 300.0<br> YOSHIDA 3 # 3 is the default<br> &END NOSE<br> &END THERMOSTAT<br> &END MD<br><br> &FREE_ENERGY<br> &METADYN<br> DO_HILLS<br> NT_HILLS 100<br> WW [kcalmol] 0.5<br> &METAVAR<br> SCALE 0.2<br> COLVAR 1<br> &WALL<br> TYPE QUADRATIC<br> POSITION [angstrom] 3.0<br> &QUADRATIC<br> DIRECTION WALL_PLUS<br> K [kcalmol] 100.0<br> &END<br> &END<br> &END METAVAR<br> &METAVAR<br> SCALE 0.2<br> COLVAR 2<br> &WALL<br> TYPE QUADRATIC<br> POSITION [angstrom] 3<br> &QUADRATIC<br> DIRECTION WALL_PLUS<br> K [kcalmol] 100.0<br> &END<br> &END<br> &END METAVAR<br><br> &PRINT<br> &COLVAR<br> COMMON_ITERATION_LEVELS 3<br> &EACH<br> MD 1<br> &END<br> &END<br> &HILLS<br> COMMON_ITERATION_LEVELS 3<br> &EACH<br> MD 1<br> &END<br> &END<br> &END<br><br> &END METADYN<br> &END<br><br> &PRINT<br> &RESTART_HISTORY<br> &EACH<br> MD 100<br> &END<br> &END RESTART_HISTORY<br> &VELOCITIES<br> &EACH<br> MD 1<br> &END<br> &END<br> # Normal restart file<br> &RESTART<br> &EACH<br> MD 1<br> &END<br> &END RESTART<br> &END PRINT<br>&END MOTION<br><br>&FORCE_EVAL<br> METHOD Quickstep ! Electronic structure method (DFT,...)<br> &DFT<br> CHARGE = 0<br> MULTIPLICITY = 2<br> LSD<br> BASIS_SET_FILE_NAME BASIS_MOLOPT.dat<br> POTENTIAL_FILE_NAME GTH_POTENTIALS.dat<br> # if WFN restart is required<br> WFN_RESTART_FILE_NAME 1a.wfn<br> &MGRID<br> #CUTOFF 1000<br> CUTOFF 360<br> NGRIDS 4<br> REL_CUTOFF 60<br> &END MGRID<br> &QS<br> METHOD GPW<br> EPS_DEFAULT 1.0E-10 # 1.0E-10 is the default<br> &END QS<br> &SCF<br> SCF_GUESS RESTART<br> EPS_SCF 1.0E-5 # 1.0E-5 is the default<br> MAX_SCF 600 # 50 is the default<br> &OT<br> MINIMIZER CG<br> PRECONDITIONER FULL_ALL<br> LINESEARCH 3PNT<br> &END<br> &OUTER_SCF<br> EPS_SCF 1.0E-5 # 1.0E-5 is the default<br> MAX_SCF 20 # Keep > 100 when OT is on<br> &END<br> &END SCF <br> &XC<br> &XC_FUNCTIONAL PBE<br> &END XC_FUNCTIONAL<br> &vdW_POTENTIAL<br> DISPERSION_FUNCTIONAL PAIR_POTENTIAL # POTENTIAL_TYPE is alias to DISPERSION_FUNCTIONAL<br> &PAIR_POTENTIAL<br> TYPE DFTD3<br> PARAMETER_FILE_NAME dftd3.dat<br> REFERENCE_FUNCTIONAL PBE<br> &END PAIR_POTENTIAL<br> &END vdW_POTENTIAL<br> &END XC<br> &POISSON ! Solver requested for non periodic calculations<br> PERIODIC NONE ! Type of solver<br> POISSON_SOLVER MT<br> &END POISSON<br> &END DFT <br> &SUBSYS<br> &CELL<br> <span> </span>A 20.0000000 0.00000000 0.00000000<br> <span> </span>B 0.00000000 20.0000000 0.00000000<br> <span> </span>C 0.00000000 0.00000000 20.00000000<br><br> PERIODIC NONE ! Non periodic calculations. That's why the POISSON section is needed<br> &END CELL<br> &TOPOLOGY ! Section used to center the atomic<br> COORD_FILE_FORMAT xyz<br> COORD_FILE_NAME <a href="http://1a.xyz/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=fr&q=http://1a.xyz/&source=gmail&ust=1739870180589000&usg=AOvVaw3K0WW9abwk_8xCosYXPq_Z">1a.xyz</a><br> &CENTER_COORDINATES<br> &END<br> &END<br> &KIND C<br> ELEMENT C<br> BASIS_SET DZVP-MOLOPT-SR-GTH-q4<br> POTENTIAL GTH-PBE-q4<br> &END KIND <br> &KIND H<br> ELEMENT H<br> BASIS_SET DZVP-MOLOPT-SR-GTH-q1<br> POTENTIAL GTH-PBE-q1<br> &END KIND <br> &KIND Cl<br> ELEMENT Cl<br> BASIS_SET DZVP-MOLOPT-SR-GTH-q7<br> POTENTIAL GTH-PBE-q7<br> &END KIND<br> &KIND O<br> ELEMENT O<br> BASIS_SET DZVP-MOLOPT-SR-GTH-q6<br> POTENTIAL GTH-PBE-q6<br> &END KIND<br><br> &COLVAR<br> &DISTANCE<br> ATOMS 5 3<br> &END DISTANCE<br> &END COLVAR<br> &COLVAR<br> &DISTANCE<br> ATOMS 7 3<br> &END DISTANCE<br> &END COLVAR<br> &END SUBSYS<br>&END FORCE_EVAL<br><br><br>I have attached my input file<br></div></blockquote><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, February 14, 2025 at 3:34:42 PM UTC+5:30 Quentin Pessemesse wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hello, <br></div><div>I think you need to provide a bit more information such as the total time of your simulation, the type of system and maybe an input file. Metadynamics can be very long to converge, and it might be impossible to achieve convergence with ab initio depending on your CV for instance. If you observe crossing, it means that your CV is able to "push" the system over the barrier which is already a good sign. <br></div><div>The plumed tutorials and google groups have information on how to understand how to see if a metadynamics simulation is converged, for instance:</div><div><a href="https://groups.google.com/g/plumed-users/c/3R9CghiH8EE" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://groups.google.com/g/plumed-users/c/3R9CghiH8EE&source=gmail&ust=1739870180589000&usg=AOvVaw2R4LS7B47dgf0rYReT7iiE">https://groups.google.com/g/plumed-users/c/3R9CghiH8EE</a></div><div><a href="https://www.plumed.org/doc-v2.9/user-doc/html/master-_i_s_d_d-2.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=fr&q=https://www.plumed.org/doc-v2.9/user-doc/html/master-_i_s_d_d-2.html&source=gmail&ust=1739870180589000&usg=AOvVaw3XlmGUthliaNzYmXh0CyDU">https://www.plumed.org/doc-v2.9/user-doc/html/master-_i_s_d_d-2.html</a></div><div>There are other sampling methods that can help you achieve convergence of a free energy barrier if metadynamics does not work for your system.</div><div>Take care,</div><div>Quentin</div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">Le mercredi 12 février 2025 à 13:01:43 UTC+1, SAURABH SINGH a écrit :<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hii <br><br>I am facing a problem in metadynamics study<br><br>I am using normal metadynamics.<br>In my case I am getting the multiple recrossing, but my energy is not converging <br>I am using wall height 1 kcal/mol and sigma as 0.3 <br><br>Is it indicating issues with CV?<br><br>I will be very grateful if you can give some valuable insights<br><br>Thank you</blockquote></div></blockquote></div></blockquote></div>
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