<div dir="ltr">Dear Thomas,<div><br></div><div>Thanks for your response. My aim is to understand the solvation shell around the central MM molecule, so I kept the timestep and the equilibration length short to avoid excessive motion of QM water molecules and decomposing the solvation shell. Do you have any recommendations on how to accelerate equilibration in such a scenario?</div><div><br></div><div>Best,</div><div>Mayank</div><br>On Wednesday, August 5, 2020 at 10:57:17 AM UTC+2, tkuehne wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div style="word-wrap:break-word;line-break:after-white-space">Dear Mayank, <div><br></div><div>the y-axis of your conserved quantity plot is too coarse to judge if energy conservation is an issue at all. </div><div>Possibly it is already good enough, but in any case the integration time step error is not <a href="http://s.th" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fs.th\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE31Fcjc_BtCd1cvUBHKBBpRPbj4w';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fs.th\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE31Fcjc_BtCd1cvUBHKBBpRPbj4w';return true;">s.th</a>. you should </div><div>be concerned first and foremost, hence you can safely increase TIMESTEP. Also, since energy is an extensive </div><div>property, in my opinion the best way to look at the conserved quantity is in units of Kelvin per atom and ps. </div><div>The potential energy is a matter of your initial configuration and only shows that you haven’t equilibrated </div><div>as yet … </div><div><br></div><div>Cheers, </div><div>Thomas </div><div><div><br><blockquote type="cite"><div>Am 04.08.2020 um 08:52 schrieb mayank...@<a href="http://gmail.com" target="_blank" rel="nofollow" onmousedown="this.href='http://gmail.com';return true;" onclick="this.href='http://gmail.com';return true;">gmail.com</a> <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Qh4-RukhAgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">ma...@gmail.com</a>>:</div><br><div>Hi,<div><br></div><div>I am trying a NVT MD simulation for a QM/MM system with QM water molecules surrounding a spatially fixed MM molecule, which are in turn surrounded by MM water molecules. I am using a time step of 5 a.u. (for particular reasons) and the QM box is much smaller than compared to full MM box so within the timescale of MD simulation the QM molecules do not cross the QM box boundary. I am attaching the relevant sections of input file:</div><div>----</div><div><div> &MOTION</div><div> &MD</div><div> ENSEMBLE NVT</div><div> STEPS 10000</div><div> TIMESTEP 1.21E-01</div><div> TEMPERATURE 3.00E+02<br></div><div> &THERMOSTAT</div><div> TYPE NOSE</div><div> REGION DEFINED</div><div> &DEFINE_REGION</div><div> QM_SUBSYS ATOMIC</div><div> &END DEFINE_REGION</div><div> &DEFINE_REGION</div><div> MM_SUBSYS ATOMIC</div><div> &END DEFINE_REGION</div><div> &NOSE</div><div> TIMECON 9.99E+02</div><div> &END NOSE</div><div> &END THERMOSTAT</div></div><div><br></div><div><div> &FORCE_EVAL</div><div> METHOD QMMM</div><div> &DFT</div><div> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS</div><div> POTENTIAL_FILE_NAME ./GTH_POTENTIALS</div><div> CHARGE 0</div><div> &SCF</div><div> MAX_SCF 60</div><div> EPS_SCF 2.0E-07</div><div> SCF_GUESS RESTART</div><div> &OT T</div><div> MINIMIZER DIIS</div><div> PRECONDITIONER FULL_SINGLE_INVERSE</div><div> &END OT</div><div> &OUTER_SCF T</div><div> EPS_SCF 2.0E-07</div><div> MAX_SCF 40</div><div> &END OUTER_SCF</div><div> &PRINT</div><div> &RESTART SILENT</div><div> BACKUP_COPIES 1</div><div> &END RESTART</div><div> &END PRINT</div><div> &END SCF</div><div> &QS</div><div> EXTRAPOLATION ASPC</div><div> EXTRAPOLATION_ORDER 4</div><div> &END QS</div><div> &MGRID</div><div> CUTOFF 3.2E+02</div><div> COMMENSURATE T</div><div> &END MGRID</div><div> &XC</div><div> DENSITY_CUTOFF 1.0E-10</div><div> GRADIENT_CUTOFF 1.0E-10</div><div> TAU_CUTOFF 1.0E-10</div><div> &XC_GRID</div><div> XC_SMOOTH_RHO NN50</div><div> XC_DERIV SPLINE2_SMOOTH</div><div> &END XC_GRID</div><div> &XC_FUNCTIONAL NO_SHORTCUT</div><div> &PBE T</div><div> PARAMETRIZATION REVPBE</div><div> &END PBE</div><div> &END XC_FUNCTIONAL</div><div> &VDW_POTENTIAL</div><div> POTENTIAL_TYPE PAIR_POTENTIAL</div><div> &PAIR_POTENTIAL</div><div> R_CUTOFF 1.9E+01</div><div> TYPE DFTD3</div><div> PARAMETER_FILE_NAME ./dftd3.dat</div><div> REFERENCE_FUNCTIONAL revPBE</div><div> CALCULATE_C9_TERM T</div><div> REFERENCE_C9_TERM T</div><div> LONG_RANGE_CORRECTION F</div><div> &END PAIR_POTENTIAL</div><div> &END VDW_POTENTIAL</div><div> &END XC</div><div> &END DFT</div><div> &MM</div><div> &FORCEFIELD</div><div> ...</div><div> &END FORCEFIELD</div><div> &POISSON</div><div> &EWALD</div><div> EWALD_TYPE SPME</div><div> RCUT 1.2E+01</div><div> ALPHA 2.917E-01</div><div> GMAX 75</div><div> O_SPLINE 4</div><div> &END EWALD</div><div> &END POISSON</div><div> &END MM</div><div> &QMMM</div><div> E_COUPL GAUSS</div><div> USE_GEEP_LIB 6</div><div> NOCOMPATIBILITY T</div><div> CENTER NEVER</div><div> INITIAL_TRANSLATION_VECTOR 0.0E+00 0.0E+00 0.0E+00</div><div> &QM_KIND O</div><div> MM_INDEX ...</div><div> &END QM_KIND</div><div> &QM_KIND H</div><div> MM_INDEX ...</div><div> &END QM_KIND</div><div> &MM_KIND H</div><div> RADIUS 4.4E-01</div><div> &END MM_KIND</div><div> &MM_KIND O</div><div> RADIUS 1.2E+00</div><div> &END MM_KIND</div><div> .....</div><div> &CELL</div><div> ABC 4.0E+01 3.0E+01 3.0E+01</div><div> PERIODIC XYZ</div><div> &END CELL</div><div> &PERIODIC</div><div> GMAX 5.0E-01</div><div> &MULTIPOLE ON</div><div> RCUT 1.2E+01</div><div> EWALD_PRECISION 1.0E-08</div><div> ANALYTICAL_GTERM T</div><div> &END MULTIPOLE</div><div> &END PERIODIC</div><div> &END QMMM</div><div> &SUBSYS</div><div> &CELL</div><div> A 5.0E+01 0.0E+00 0.0E+00</div><div> B 0.0E+00 4.0E+01 0.0E+00 </div><div> C 0.0E+00 0.0E+00 4.0E+01</div><div> MULTIPLE_UNIT_CELL 1 1 1</div><div> &END CELL</div><div> &COORD</div></div><div><br></div><div>-------</div><div><br></div><div>With this setup for the production run I obtained the following trends for the potential and constant quantity as the graphs attached here. I have tested the QM setup for a fully QM calculation on bulk water, which works fine. My main aim here is to reduce the energy drift for the QM/MM system, so is there any other aspect of the calculation should I take care to reduce the drift? Any suggested corrections for the QM/MM file would also be helpful.</div><div><br></div><div>Best Regards,</div><div>Mayank Dodia</div><div><br></div><div><br></div><div><br></div><div><br></div>
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<span><const_quantity.png></span><span><pot_enr.<wbr>png></span></div></blockquote></div><br></div><br><br><div>
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