<div dir="ltr"><div class="gmail_default" style="color:#000000">Dear
Juerg
and Thomas,</div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style="color:#000000">Thank you so much for your helpful suggestions. I will try to modify my input file accordingly and repeat the calculation.</div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style="color:#000000">Best,</div><div class="gmail_default" style="color:#000000">Mostafa<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 29, 2020 at 10:07 AM Thomas Kühne <<a href="mailto:tku...@gmail.com">tku...@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 Mostafa, <div><br></div><div>your simulation is way too short. Equilibrating the density needs many dozens of ps of simulation, </div><div>and much more so since you are using the default 1ps time constant for the barostat. My </div><div>suggestion is to reduce that to 100 fs and rerun your simulation for at least 25 ps. Also, you were </div><div>missing to add the VdW contribution of the wB97X XC functional. </div><div><br></div><div>Cheers, </div><div>Thomas</div><div><div><br><blockquote type="cite"><div>Am 29.07.2020 um 14:57 schrieb Abedi, Mostafa <<a href="mailto:mostaf...@brown.edu" target="_blank">mostaf...@brown.edu</a>>:</div><br><div><div dir="ltr"><div class="gmail_default">Hi Everyone,</div><div class="gmail_default">I've performed NpT AIMD simulations for a system containing 8 CH4 molecules. The system was equilibrated using 2 ps NVT (300K) followed by 2 ps NVE. For some reason, the predicted density keeps decreasing and getting away from the correct value (The correct density is 0.232 g/cm3):</div><div class="gmail_default"><br></div><div class="gmail_default"><i><b> Time evaluation of density for a box of 8 CH4 at 300 K and 400 bar</b></i><br></div><div class="gmail_default"><div><span id="gmail-m_-3650968519677037007cid:ii_kd7cji820"><density.PNG></span><br></div><div>The wB97XD/TZVP-MOLOPT-GTH level of theory was used for the electronic structure part. Unfortunately, there is not much in the literature for this system (or similar systems) to get some ideas for the level of theory. To my mind, it could be due to the wrong prediction of the intermolecular repulsive interactions (vdW dispersion forces). But, there might be some other parameters in the simulations that can cause this issue. Any suggestions or advice for fixing this issue would be greatly appreciated. Many thanks. <br></div><div><br></div><div>Best,</div><div>Mostafa</div><div><br></div><div>Input file:</div><div><i><span style="font-family:times new roman,serif">&GLOBAL<br> PROJECT methane<br> RUN_TYPE MD <br> WALLTIME 10000000<br> IOLEVEL LOW <br>&END GLOBAL<br></span></i></div><div><i><span style="font-family:times new roman,serif"><br></span></i></div><div><i><span style="font-family:times new roman,serif">&FORCE_EVAL<br> STRESS_TENSOR ANALYTICAL<br> METHOD Quickstep<br> &DFT<br> BASIS_SET_FILE_NAME BASIS_MOLOPT<br> POTENTIAL_FILE_NAME GTH_POTENTIALS <br> CHARGE 0<br> MULTIPLICITY 1<br> &MGRID<br> CUTOFF [Ry] 400 <br> &END<br> &QS<br> METHOD GPW <br> EPS_DEFAULT 1.0E-10 <br> EXTRAPOLATION ASPC <br> &END<br> &POISSON<br> PERIODIC XYZ <br> POISSON_SOLVER PERIODIC<br> &END<br> &SCF <br> &PRINT<br> &RESTART OFF<br> &END<br> &END <br> SCF_GUESS ATOMIC <br> MAX_SCF 300<br> EPS_SCF 1.0E-6 <br> &OT<br> PRECONDITIONER FULL_SINGLE_INVERSE<br> MINIMIZER CG<br> &END OT<br> &OUTER_SCF <br> MAX_SCF 300<br> EPS_SCF 1.0E-6 <br> &END<br> &END SCF<br> &XC<br> &XC_FUNCTIONAL<br> &LIBXC<br> FUNCTIONAL XC_HYB_GGA_XC_WB97X_D<br> &END LIBXC<br> &END XC_FUNCTIONAL<br> &END XC<br> &END DFT<br> &SUBSYS<br> &CELL <br> ABC [angstrom] 9.71 9.71 9.71<br> PERIODIC XYZ<br> &END CELL<br> &TOPOLOGY<br> COORD_FILE_NAME <a href="http://methane.xyz/" target="_blank">methane.xyz</a><br> COORD_FILE_FORMAT XYZ<br> &END<br> &KIND H<br> ELEMENT H<br> BASIS_SET TZVP-MOLOPT-GTH<br> POTENTIAL GTH-PBE-q1<br> &END KIND<br> &KIND C<br> ELEMENT C<br> BASIS_SET TZVP-MOLOPT-GTH<br> POTENTIAL GTH-PBE-q4<br> &END KIND<br> &END SUBSYS<br> &PRINT<br> &FORCES ON<br> FILENAME forces <br> &END<br> &END<br>&END FORCE_EVAL<br><br>&MOTION<br> &GEO_OPT<br> OPTIMIZER BFGS <br> MAX_ITER 1000<br> MAX_DR [bohr] 0.003 <br> &BFGS<br> &END<br> &END<br> &MD<br> ENSEMBLE NPT_I<br> STEPS 15000<br> TIMESTEP 0.5<br> TEMPERATURE 300<br> &BAROSTAT<br> PRESSURE 400<br> &END BAROSTAT<br> &THERMOSTAT<br> REGION MASSIVE<br> TYPE CSVR<br> &CSVR<br> TIMECON 50<br> &END CSVR<br> &END THERMOSTAT<br> &END MD<br> &PRINT<br> &TRAJECTORY<br> FORMAT XYZ <br> &END<br> &CELL<br> FILENAME cell <br> &END<br> &END<br>&END MOTION</span></i><br></div> </div><div class="gmail_default"><br></div></div><div><br></div>
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