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Ciao Nick,<div><br><div><div>On 10 Mar 2008, at 22:28, Nichols A. Romero wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">To elaborate on what Teo said, (he can correct me if I am wrong)<br><br>In NVT, the total energy of the *real sytem + thermostat* should be conserved.<br>(I don't remember if CP2K outputs this quantity, but most codes should).</blockquote>Exactly.. and this quantity is what we call CONSERVED QNTY or you can find the same number in the 6th column of the .ener file.</div><div><br><blockquote type="cite">The total energy of just the real system (atoms,molecules,etc.) should have a mean value (after equilibration) with fluctuations proportional to 1/sqrt(N) (or something like that).<br><br>If the total energy of the real system increases or decreases without bounds, then there is something wrong.<br> Or maybe you are near some phase transition.</blockquote>Absolutely correct. In this case I think that the forces computed have something wrong.. </div><div>Let me explain better once for all. The SCF module is still not fully completed. The most important part missing is </div><div>the ewald for the coulomb part (we have a project going on for that, so it should be hopefully fixed one day ;-) ).</div><div>This means that at the moment the coulomb is evaluated through a neighbor lists. </div><div>This creates ENORMOUS problem if you condensed phases (same problem of using a cutoff to truncate the electrostatic interactions </div><div>in force field based calculations) but also if you do big molecules (and this is her case) and don't set properly</div><div>the parameter I wan mentioning in my last e-mail.</div><div>What happens here is that during the MD you've interactions turned on and off at the boundary and the contribution is such that</div><div>you observe a drift. </div><div><br></div><div>Of course I could be wrong.. but since the nose-hoover thermostat has been so extensively tested i would rarely look for a bug in it ;-)</div><div><br class="webkit-block-placeholder"></div><div>Teo</div><div><br class="webkit-block-placeholder"></div><div><blockquote type="cite"><br> <br><div class="gmail_quote">On Mon, Mar 10, 2008 at 4:37 PM, Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> Ciao Diederica,<br> <div class="Ih2E3d"><br> ><br> > These are added, as an attachment this time<br> <br> </div>Thanks.. will look into this problem ASAP.<br> <div class="Ih2E3d"><br> > I'm modelling an isolated molecule, it should fit in the box. Using<br> > NVE without temperature rescaling, with an analogue structure, an<br> > energy drift was observed, that got worse after about 20 ps, though<br> > no non-convergence was observed. The input file and an energy-plot<br> > are added.<br> </div>If you have a drift with NVE this means that energy and forces are<br> not consistent.. or (what I assume) that the cutoff for the coulomb<br> interactions is not large enough..<br> <br> Please put all of the RC_COULOMB and RC_INTERACTION and RC_RANGE to<br> 50.0.<br> You've the problem that in your cell the standard range (24 bohr)<br> does not fully cover the extension of your molecule (more than 26 bohr).<br> Use a larger box (30.0 Angstrom) and set the above keywords to 50.0<br> bohr.<br> You should not see any jump in the energy (or drift)..<br> <div class="Ih2E3d"><br> > The potential and kinetic energy are conserved indeed, but the<br> > conserved quantity is not<br> </div>Sorry to disprove you, but it is not possible that in an NVT you have<br> kinetic and potential conserved, since the thermostat<br> is continuously exchanging energy with the system. I't s a matter of<br> concept.. we may discuss about the magnitude of the<br> thermostat energy.. but that's another story..<br> <br> Cheers<br> teo<br> <div class="Ih2E3d"><br> <br> <br> ><br> ><br> ><br> > For the next time, can you please put tables and input files as<br> > attachment (maybe .tgz) so that the formatting of mail readers are<br> > not changed and the input files not digested ? Thanks..<br> ><br> > Ciao,<br> > teo<br> ><br> > Thanks for helping!<br> ><br> > Greetz,<br> > Diederica<br> ><br> ><br> ><br> ><br> > ><br> </div>> <mailcp2k.tgz><br> <div><div></div><div class="Wj3C7c"><br> <br> <br> </div></div></blockquote></div><br><br clear="all"><br>-- <br>Nichols A. Romero, Ph.D.<br>DoD User Productivity Enhancement and Technology Transfer (PET) Group<br>High Performance Technologies, Inc.<br>Reston, VA<br>443-567-8328 (C)<br> 410-278-2692 (O)<br> <br> <br></blockquote></div><br></div></body></html>