<div dir="ltr"><div class="gmail_default" style="color:#000000">Dear
Marcella,</div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style="color:#000000">Many thanks for your help. Now, I understand it. I've found a way to wrap the coordinate into the box using VMD: <br></div><div class="gmail_default" style="color:#000000">
<div class="gmail_extra"><span style="font-family:times new roman,serif">pbc set {xxx xxx xxx} -all <span class="gmail_default" style="color:rgb(0,0,0)"> # the "xxx" is the length of the box
</span></span></div><div class="gmail_extra"><span style="font-family:times new roman,serif">pbc box</span></div><div class="gmail_extra"><span style="font-family:times new roman,serif">pbc wrap -all <br></span></div><div class="gmail_extra"><span style="font-family:times new roman,serif"><br></span></div><div class="gmail_extra"><span style="font-family:times new roman,serif"><span class="gmail_default" style="color:rgb(0,0,0)"><span style="font-family:arial,sans-serif">This works well for the NVE and NVT simulations that the length of the box is fixed, but it is not a case for the NpT simulation box, where the volume changes. </span></span><span class="gmail_default" style="color:rgb(0,0,0)"><span style="font-family:arial,sans-serif">Do you have any idea how that would be for the NpT one? I greatly appreciate your help. </span></span><br></span></div><div class="gmail_extra"><span style="font-family:times new roman,serif"><br></span></div><div class="gmail_extra"><span style="font-family:arial,sans-serif"><span class="gmail_default" style="color:rgb(0,0,0)">Thanks,</span></span></div><div class="gmail_extra"><span style="font-family:times new roman,serif"><span style="font-family:arial,sans-serif"><span class="gmail_default" style="color:rgb(0,0,0)">Mostafa</span></span><br></span></div>
</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 22, 2020 at 10:25 AM Marcella Iannuzzi <<a href="mailto:marci...@gmail.com">marci...@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">Dear Mostafa<div><br></div><div>CP2K does not wrap the coordinates into the primary box, but works with the absolute coordinates.</div><div>The PBC are anyway internally applied by calculating energy and forces, hence the interaction field in which your molecules move is correct. </div><div>To verify the actual situation within the simulation box just apply PBC when using the visualisation tool of your choice.</div><div><br></div><div>Regards</div><div>Marcella</div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, July 22, 2020 at 3:47:52 PM UTC+2 <a href="mailto:mos...@brown.edu" target="_blank">mos...@brown.edu</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 dir="ltr"><div class="gmail_default" style="color:rgb(0,0,0)">Hi Everyone,</div><div class="gmail_default" style="color:rgb(0,0,0)">I am trying to perform AIMD for a periodic system containing 8 CH4 molecules. Everything goes well, but after a few hundred steps, methane molecules start to leave the box. This is really strange behavior because the simulation is running under PBC and if one molecule leaves the box, one of its images must enter through the opposite face with exactly the same way and direction. But this is not happening in my simulations. So, it seems PBC is not working. I believe something is wrong in my input file, but I can not figure out what it is. I greatly appreciate it if someone could help me to fix this issue. Many thanks.
<br></div><div class="gmail_default" style="color:rgb(0,0,0)"><br></div><div class="gmail_default" style="color:rgb(0,0,0)"><span style="font-family:times new roman,serif">&GLOBAL<br> PROJECT methane<br> RUN_TYPE MD <br> WALLTIME 1000000<br> PRINT_LEVEL MEDIUM<br>&END GLOBAL<br></span></div><div class="gmail_default" style="color:rgb(0,0,0)"><span style="font-family:times new roman,serif"><br></span></div><div class="gmail_default" style="color:rgb(0,0,0)"><span style="font-family:times new roman,serif">&FORCE_EVAL<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 30<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 10<br> EPS_SCF 1.0E-6 <br> &END<br> &END SCF<br> &XC<br> &XC_FUNCTIONAL<br> &PBE<br> &END<br> &END XC_FUNCTIONAL<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> &SUBSYS<br> &CELL <br> ABC [angstrom] 9.2 9.2 9.2<br> PERIODIC XYZ<br> &END CELL<br> &TOPOLOGY<br> COORD_FILE_NAME <a href="http://methane.xyz" rel="nofollow" target="_blank">methane.xyz</a><br> COORD_FILE_FORMAT XYZ<br> &END<br> &KIND H<br> ELEMENT H<br> BASIS_SET SZV-MOLOPT-GTH<br> POTENTIAL GTH-PBE-q1<br> &END KIND<br> &KIND C<br> ELEMENT C<br> BASIS_SET SZV-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 NVE<br> STEPS 10000<br> TIMESTEP 0.5<br> TEMPERATURE 500<br> &END MD<br> &PRINT<br> &CELL<br> FILENAME cell <br> &END<br> &END<br>&END MOTION</span><br><br></div><div class="gmail_default" style="color:rgb(0,0,0)"><br></div><div class="gmail_default" style="color:rgb(0,0,0)">Best,</div><div class="gmail_default" style="color:rgb(0,0,0)">Mostafa<br></div><div class="gmail_default" style="color:rgb(0,0,0)"><div><div><br></div></div></div></div>
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