<div dir="ltr">Hi Matt, <div><br></div><div>thank you very much for answering a part of my questions (despite your 12 hour flight), really appreciate it. </div><div><br></div><div>Best wishes,</div><div>Jadzia</div><div><br></div><div><br></div><div><br><br>On Saturday, September 30, 2017 at 10:26:49 PM UTC+2, Matt W wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi,<div><br></div><div>I'm a zombie after 12 hours on a plane, so may contain mistakes:<br><br>On Wednesday, September 27, 2017 at 5:29:47 PM UTC+4, Jadzia wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi everyone, <div><br></div><div>I am trying to simulate a system with an isolated molecule, therefore I need a non-periodic setup. I have read the previous posts about the topic, but there are a number of questions open. They are both for the wavelet and the MT Poisson solver. </div><div><br></div><div><b>1) System size</b></div><div>My simulations will be quite long (both MM and QM) and due to the movement of the molecule, to my understanding it needs to be avoided that the molecule leaves the box. Will it be fine if I set the box size to 1000 Angstrom for security reasons or is this not recommended? </div><div><br></div></div></blockquote><div>Definitely not fine for QM, because you will run out of memory - we store densities etc on grids that grow with the volume of the system. MM you could be OK if totally non-periodic.</div><div> </div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><b>2) Periodic cells</b></div><div>This question is closely related to question 1). If I set the Poisson solver to non-periodic, could one set the CELL to periodic, and thus solve the problem that the molecule leaves the box?</div><div><br></div></div></blockquote><div>This would work for MM, I think. I suspect that MT doesn't care where the molecule is in the box, but haven't every tried it.</div><div> </div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><b>3) Ewald methods</b></div><div>Also closely related to question 1). If I set the box size to 1000, even with Ewald as Poisson solver the system should be effectively non-periodic due to the large distance, right? Would this be a plausible alternative to the MT or wavelet solvers?</div><div><br></div></div></blockquote><div>Yes, at least for neutral systems, but it would be extremely expensive.</div><div> </div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><b>4) Mixed force evaluations</b></div><div>In the case that I have a mixed force evaluation setup and use the Wavelet solver (see the config file below), do I need to include the &CENTER_COORDINATES section also in the mixed force eval section, or only in the real force evaluation section?</div><div><br></div></div></blockquote><div>No idea. Test _very_ carefully.</div><div> </div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><b>5) MT solver for periodic systems</b></div><div>Is the MT solver only for nonperiodic systems in CP2K, or does it also work for periodic systems? In the publication it is at least written it works for periodic systems and even with ewald/spme. </div><div><br></div></div></blockquote><div>Don't know, try it. </div><div> </div><div>Matt</div><div><br></div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div>Looking forward to hearing from you.</div><div><br></div><div>Best wishes,</div><div>Jadzia</div><font size="1"><br><br></font><div dir="ltr"><font size="1">&GLOBAL</font></div><div dir="ltr"><font size="1"> PROJECT system</font></div><div dir="ltr"><font size="1"> RUN_TYPE md</font></div><div dir="ltr"><font size="1"> PRINT_LEVEL medium</font></div><div dir="ltr"><font size="1">&END global</font></div><div dir="ltr"><font size="1"><br></font></div><div dir="ltr"><font size="1">&MOTION</font></div><div dir="ltr"><font size="1"> &MD</font></div><div dir="ltr"><font size="1"> ENSEMBLE langevin</font></div><div dir="ltr"><font size="1"> &LANGEVIN </font></div><div dir="ltr"><font size="1"> GAMMA [fs^-1] 1.0E-3 # "Langevin" gamma (adapt for your system) </font></div><div dir="ltr"><font size="1"> &END LANGEVIN</font></div><div dir="ltr"><font size="1"> STEPS 5000000</font></div><div dir="ltr"><font size="1"> TIMESTEP 0.5</font></div><div dir="ltr"><font size="1"> TEMPERATURE 300.0</font></div><div dir="ltr"><font size="1"> &END MD </font></div><div dir="ltr"><font size="1">&END MOTION</font></div><div dir="ltr"><font size="1"><br></font></div><div dir="ltr"><font size="1">&MULTIPLE_FORCE_EVALS</font></div><div dir="ltr"><font size="1"> FORCE_EVAL_ORDER 2 3</font></div><div dir="ltr"><font size="1"> MULTIPLE_SUBSYS true</font></div><div dir="ltr"><font size="1">&END</font></div><div dir="ltr"><font size="1"><br></font></div><div dir="ltr"><font size="1">&FORCE_EVAL</font></div><div dir="ltr"><font size="1"> STRESS_TENSOR analytical</font></div><div dir="ltr"><font size="1"> METHOD mixed</font></div><div dir="ltr"><font size="1"> &MIXED</font></div><div dir="ltr"><font size="1"> MIXING_TYPE genmix</font></div><div dir="ltr"><font size="1"> &GENERIC</font></div><div dir="ltr"><font size="1"> VARIABLES a b</font></div><div dir="ltr"><font size="1"> MIXING_FUNCTION a+b</font></div><div dir="ltr"><font size="1"> &END</font></div><div dir="ltr"><font size="1"> @include cp2k.in.mapping</font></div><div dir="ltr"><font size="1"> &END</font></div><div dir="ltr"><font size="1"> &SUBSYS</font></div><div dir="ltr"><font size="1"> &TOPOLOGY</font></div><div dir="ltr"><font size="1"> &CENTER_COORDINATES </font></div><div dir="ltr"><font size="1"> &END </font></div><div dir="ltr"><font size="1"> CONNECTIVITY off</font></div><div dir="ltr"><font size="1"> COORDINATE pdb</font></div><div dir="ltr"><font size="1"> COORD_FILE_NAME system.pdb</font></div><div dir="ltr"><font size="1"> &END TOPOLOGY</font></div><div dir="ltr"><font size="1"> &CELL</font></div><div dir="ltr"><font size="1"> PERIODIC NONE</font></div><div dir="ltr"><font size="1"> ABC 20 20 20 </font></div><div dir="ltr"><font size="1"> &END CELL</font></div><div dir="ltr"><font size="1"> &END SUBSYS</font></div><div dir="ltr"><font size="1">&END FORCE_EVAL</font></div><div dir="ltr"><font size="1"><br></font></div><div dir="ltr"><font size="1">&FORCE_EVAL</font></div><div dir="ltr"><font size="1"> STRESS_TENSOR analytical</font></div><div dir="ltr"><font size="1"> METHOD fist</font></div><div dir="ltr"><font size="1"> &MM</font></div><div dir="ltr"><font size="1"> &FORCEFIELD</font></div><div dir="ltr"><font size="1"> PARM_FILE_NAME system1.prm</font></div><div dir="ltr"><font size="1"> PARMTYPE chm</font></div><div dir="ltr"><font size="1"> &SPLINE</font></div><div dir="ltr"><font size="1"> EMAX_SPLINE 100000</font></div><div dir="ltr"><font size="1"> RCUT_NB 12.</font></div><div dir="ltr"><font size="1"> &END</font></div><div dir="ltr"><font size="1"> &END FORCEFIELD </font></div><div dir="ltr"><font size="1"> &POISSON</font></div><div dir="ltr"><font size="1"> POISSON_SOLVER WAVELET</font></div><div dir="ltr"><font size="1"> PERIODIC NONE</font></div><div dir="ltr"><font size="1"> &EWALD </font></div><div dir="ltr"><font size="1"> EWALD_TYPE NONE </font></div><div dir="ltr"><font size="1"> &END EWALD </font></div><div dir="ltr"><font size="1"> &END POISSON</font></div><div dir="ltr"><font size="1"> &END MM</font></div><div dir="ltr"><font size="1"> &SUBSYS</font></div><div dir="ltr"><font size="1"> &CELL</font></div><div dir="ltr"><font size="1"> PERIODIC NONE</font></div><div dir="ltr"><font size="1"> ABC 20 20 20</font></div><div dir="ltr"><font size="1"> &END CELL</font></div><div dir="ltr"><font size="1"> &TOPOLOGY</font></div><div dir="ltr"><font size="1"> &CENTER_COORDINATES </font></div><div dir="ltr"><font size="1"> &END </font></div><div dir="ltr"><font size="1"> COORDINATE pdb</font></div><div dir="ltr"><font size="1"> COORD_FILE_NAME system1.pdb</font></div><div dir="ltr"><font size="1"> CONN_FILE_FORMAT psf</font></div><div dir="ltr"><font size="1"> CONN_FILE_NAME system1.psf</font></div><div dir="ltr"><font size="1"> &END TOPOLOGY</font></div><div dir="ltr"><font size="1"> &END SUBSYS</font></div><div dir="ltr"><font size="1">&END FORCE_EVAL</font></div><div dir="ltr"><font size="1"><br></font></div><div dir="ltr"><font size="1">&FORCE_EVAL</font></div><div dir="ltr"><font size="1"> STRESS_TENSOR analytical</font></div><div dir="ltr"><font size="1"> METHOD fist</font></div><div dir="ltr"><font size="1"> &MM</font></div><div dir="ltr"><font size="1"> &FORCEFIELD</font></div><div dir="ltr"><font size="1"> PARM_FILE_NAME system2.prm</font></div><div dir="ltr"><font size="1"> PARMTYPE chm</font></div><div dir="ltr"><font size="1"> &SPLINE</font></div><div dir="ltr"><font size="1"> EMAX_SPLINE 100000</font></div><div dir="ltr"><font size="1"> RCUT_NB 12.</font></div><div dir="ltr"><font size="1"> &END</font></div><div dir="ltr"><font size="1"> &END FORCEFIELD </font></div><div dir="ltr"><font size="1"> &POISSON</font></div><div dir="ltr"><font size="1"> POISSON_SOLVER WAVELET</font></div><div dir="ltr"><font size="1"> PERIODIC NONE</font></div><div dir="ltr"><font size="1"> &EWALD </font></div><div dir="ltr"><font size="1"> EWALD_TYPE NONE </font></div><div dir="ltr"><font size="1"> &END EWALD </font></div><div dir="ltr"><font size="1"> &END POISSON</font></div><div dir="ltr"><font size="1"> &END MM</font></div><div dir="ltr"><font size="1"> &SUBSYS</font></div><div dir="ltr"><font size="1"> &CELL</font></div><div dir="ltr"><font size="1"> PERIODIC NONE</font></div><div dir="ltr"><font size="1"> ABC 20 20 20</font></div><div dir="ltr"><font size="1"> &END CELL</font></div><div dir="ltr"><font size="1"> &TOPOLOGY</font></div><div dir="ltr"><font size="1"> &CENTER_COORDINATES </font></div><div dir="ltr"><font size="1"> &END </font></div><div dir="ltr"><font size="1"> COORDINATE pdb</font></div><div dir="ltr"><font size="1"> COORD_FILE_NAME system2.pdb</font></div><div dir="ltr"><font size="1"> CONN_FILE_FORMAT psf</font></div><div dir="ltr"><font size="1"> CONN_FILE_NAME system2.psf</font></div><div dir="ltr"><font size="1"> &END TOPOLOGY</font></div><div dir="ltr"><font size="1"> &END SUBSYS</font></div><div dir="ltr"><font size="1">&END FORCE_EVAL</font></div></div></blockquote></div></div></blockquote></div></div>