<div>hi</div>
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<div>thanks a lot for all the explanations! The MD is running well now</div>
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<div>greetz,</div>
<div>Diederica<br><br></div>
<div class="gmail_quote">On Mon, Mar 10, 2008 at 10:37 PM, Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote:<br>
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<div style="WORD-WRAP: break-word">Ciao Nick,
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<div>On 10 Mar 2008, at 22:28, Nichols A. Romero wrote:</div><br>
<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>
</div>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>
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<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></div>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>
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<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>
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<div>Teo</div>
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<div class="gmail_quote">On Mon, Mar 10, 2008 at 4:37 PM, Teodoro Laino <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><br>Ciao Diederica,<br>
<div><br>><br>> These are added, as an attachment this time<br><br></div>Thanks.. will look into this problem ASAP.<br>
<div><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><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><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>
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<div><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></div></div>
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