<div><br></div><div><br></div><div><br></div>For the specific case<div><br></div><div>time metavar1 metavar2 metavar3 CV1 CV2 CV3 FH1 FH2 FH3 MTDF1 MTDF2 MTDF3 WF1 WF2 WF3 VEL1 VEL2 VEL3 HPOT MTDPOT WALLPOT TEMP</div><div>0.0 2.71770373 1.42316747 0.11550959 2.71061596 1.42089234 0.11424663 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00021431 0.00006879 0.00003819 0.00000000 0.00000000 0.00000000 300.00000000<br><br></div><div><br></div><div>where FH is the force contribution on metavar from the harmonic potential, MTDF is the force contribution from the MTD potential, WF is the force contribution from the wall potential</div><div><br></div><div>The rest should be selfexplaining.</div><div>Regards</div><div>Marcella</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, November 2, 2022 at 9:21:41 AM UTC+1 alh...@gmail.com 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 dir="ltr"><div dir="ltr">Dear Marcella, <div><br></div><div>Thank you very much for your reply. I found a few papers that discuss the tuning of the force constants, e.g., Ensing et al., (J. Phys. Chem. B 2005, 109, 6676-6687). From what I understand, the force constant has to be tuned such that the path of the fictitious particle is not that far away from the real CV path. So I need to prepare some data of the fictitious particle (with test runs). I would expect these data to be stored in a file called XXX_COLVAR.metadynLog.</div><div><br></div><div>In the example you explained that columns in the metadynLog file are CVs, gradients of the bias potential wrt CVs, gradients of the wall wrt CVs, values of the bias potentials, values of the wall potentials.</div><div><br></div><div>I would expect if a Lagrangian MTD is run, the coordinates of fictitious particle would be monitored in the metadynLog.</div><div><br></div><div>QUESTION: what are the columns in the metadynLog file for a Lagrangian MTD</div><div><br></div><div>thanks, </div><div><br></div><div>Alh,</div><div><br></div><div>------------------</div><div><br></div><div>(the example you provided is below, I would guess the final one is temp)</div><div><br></div><div> 0.0 2.71770373 1.42316747 0.11550959 2.71061596 1.42089234 0.11424663 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00021431 0.00006879 0.00003819 0.00000000 0.00000000 0.00000000 300.00000000</div><div> 0.8 2.72482415 1.42536380 0.11672755 2.71045717 1.41982383 0.11363373 -0.01811640 -0.01003091 -0.00562756 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00021529 0.00006641 0.00003683 0.00008769 0.00000000 0.00000000 300.00000000</div><div> 1.6 2.73206759 1.42720809 0.11779474 2.71219970 1.41629628 0.11236277 -0.03156113 -0.02720256 -0.01309435 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00021901 0.00005576 0.00003227 0.00035113 0.00000000 0.00000000 300.00000000</div><div><br></div><div><br></div><div>with the input file:</div><div><br></div><div><br></div><div>&FREE_ENERGY</div><div> &METADYN</div><div> DO_HILLS </div><div> NT_HILLS 100</div><div> WW 2.0e-3</div><div> LAGRANGE</div><div> TEMPERATURE 300.</div><div> TEMP_TOL 10.</div><div> &METAVAR</div><div> LAMBDA 2.5</div><div> MASS 30.</div><div> SCALE 0.1</div><div> COLVAR 1</div><div> &END METAVAR</div><div> &METAVAR</div><div> LAMBDA 3.0</div><div> MASS 30.0</div><div> SCALE 0.25</div><div> COLVAR 2</div><div> &END METAVAR</div><div> &METAVAR</div><div> LAMBDA 3.0</div><div> MASS 30.0</div><div> SCALE 0.25</div><div> COLVAR 3</div><div> &WALL</div><div> POSITION 0.0</div><div> TYPE QUARTIC</div><div> &QUARTIC</div><div> DIRECTION WALL_MINUS</div><div> K 100.0</div><div> &END</div><div> &END</div><div> &END METAVAR</div><div><br></div><div> &PRINT</div><div> &COLVAR</div><div> COMMON_ITERATION_LEVELS 3</div><div> &EACH</div><div> MD 1</div><div> &END</div><div> &END</div><div> &HILLS</div><div> COMMON_ITERATION_LEVELS 3</div><div> &EACH</div><div> MD 1</div><div> &END</div><div> &END</div><div> &END</div><div> &END METADYN</div><div> &END</div><div><br></div><div> &PRINT</div><div> &TRAJECTORY</div><div> &EACH</div><div> MD 50</div><div> &END</div><div> &END</div><div> &VELOCITIES OFF</div><div> &END</div><div> &RESTART</div><div> &EACH</div><div> MD 100</div><div> &END</div><div> ADD_LAST NUMERIC</div><div> &END</div><div> &RESTART_HISTORY </div><div> &EACH</div><div> MD 2000</div><div> &END</div><div> &END</div><div> &END</div><div>&END MOTION</div></div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 1, 2022 at 9:41 PM Marcella Iannuzzi <<a href data-email-masked rel="nofollow">marci...@gmail.com</a>> wrote:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Alh.<div><br></div><div>If not specified, the temperature is set to the system's temperature</div><div>The tolerance for the temperature can but must not be specified. </div><div>The units of the force constant are atomic units.</div><div>The choice of all these parameters is system dependent. </div><div>Preparatory runs to explore the system's behaviour are strongly recommended to help in choosing the proper settings.</div><div><br></div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 1, 2022 at 1:27:25 PM UTC+1 <a href data-email-masked rel="nofollow">alh...@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 all, <div><br></div><div>I want to use Lagrangian MTD to study a reaction (since the barrier appears to be high), I checked the CP2K manuals and the example at <a href="https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1&source=gmail&ust=1667464913981000&usg=AOvVaw15boNrNPsXybq5Jq4BFelB">exercises:2015_cecam_tutorial:mtd1 [CP2K Open Source Molecular Dynamics ]</a></div><div>I found that I need to specify 4 parameters for Lagrangian MTD, </div><div>(1)TEMPERATURE</div><div>(2)TEMP_TOL </div><div>and for each CV, </div><div>(3) LAMBDA</div><div>(4) MASS</div><div><br></div><div>my questions are </div><div>(1) I understand why TEMPERATURE need to be specified, but why TEMP_TOL (temperature tolerance) has to be specified?</div><div>(2) is LAMBDA the force constant for the fictitious particle? what's the unit?</div><div>(3) what would be good values for TEMP_TOL and (most importantly) LAMBDA, and, how to tune LAMBDA? </div><div><br></div><div>Thanks,</div><div><br></div><div>Alh.</div><div><br></div><div><br></div><div><br></div></blockquote></div>
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