Thanks for the quick and detailed reply, Axel. Both the systems are charge neutral, but I forgot to notice that non-equilibrated system has appreciably larger volume than equilibrated one. So yes, comparing energies like that does not mean anything definite.<div> <br></div><div>Thanks</div><div>Chetan<div><div><br><div class="gmail_quote">On Tue, Jan 24, 2012 at 9:42 PM, Axel <span dir="ltr"><<a href="mailto:akoh...@gmail.com">akoh...@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div class="im"><br><br>On Tuesday, January 24, 2012 10:02:34 PM UTC-5, Chetan Mahajan wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Friends<div> <br></div><div>I am new to cp2k or any quantum calculations, carrying out Born-Oppenheimer molecular dynamics simulations of water solvated acid-base polymer systems. I have some questions on our first output:</div> <div><br></div><div> 1. Any good reference which would explain all the terms in cp2k output? I have Essentials of Computational Chemistry by Cramer and it is pretty good, but it does not use same or all the terms as cp2k output, so it is confusing for a beginner like me. </div> </blockquote><div><br></div></div><div>the cramer book is very "essential" and does not touch a lot of what is relevant for cp2k.</div><div>a lot of the "slang" related to cp2k comes from the condensed matter physics / electronic</div> <div>structure area and is best understood, if you also gain some understanding of pure</div><div>plane wave basis set DFT calculations (e.g. in the form of car-parrinello MD).</div><div><br></div><div>a good introduction that is palatable for people with a chemistry training (there are</div> <div>other good ones, but they are more accessible to people with a strong physics</div><div>background), is in my opinion "electronic structure calculations for solid and molecules:</div><div>theory and computational methods" by jorge kohanoff. </div> <div><br></div><div>from there on, you can work your way through some of the cp2k papers</div><div>and more specific books. as a rule of the thumb you should keep in mind</div><div>that the integral of all evil things remains a constant, i.e. for every benefit</div> <div>there is a disadvantage. which means, that you have to expect to make</div><div>some serious mistakes until you get to know those problems. it is </div><div>therefore highly recommended to not start with something too difficult</div> <div>or too complex. that will just increase the number of possibilities for</div><div>errors and decrease the chances to detect them.</div><div class="im"><div><br></div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"> <div><br></div><div>2. For a classically MD equilibrated input to AIMD, initial energy is -3128.122 H, but for a random, non-equilibrated input (which by the way was my input to classical MD equilibration) to AIMD, initial energy is -3129.058 H. My question is why is energy decreasing for a non-equilibrated system? I understand we are dealing with ground-states only, but shouldn't quantum mechanical energy be higher if system is not classically equilibrated in general? Is this pointing to any error?</div> </blockquote><div><br></div></div><div>this is very difficult to say without knowing the exact difference between</div><div>your equilibrated and non-equilibrated system. do they have the same </div><div>volume? are they both neutral? if the difference is rather small, it can just</div> <div>be that what is equilibrated with a classical model has some too close</div><div>contacts for your DFT calculation. also keep in mind that (simple) DFT</div><div>(e.g. BLYP) is notoriously bad at representing dispersion interactions.</div> <div><br></div><div>it could also just mean that you may not have converged one of the </div><div>wavefunctions to the real ground state. there are many things that</div><div>can go wrong and it is difficult judge only from the total energy.</div> <div><br></div><div>axel.</div><div class="HOEnZb"><div class="h5"><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div> </div><div>Thanks</div><div>Chetan</div> <div><div><br> </div>-- <br>Chetan V Mahajan<br>PhD candidate, Ganesan Group<br>Department of Chemical Engineering<br>The University of Texas at Austin<br><br> </div> </blockquote> <p></p></div></div><span class="HOEnZb"><font color="#888888"> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msg/cp2k/-/u7HSXXG0XmMJ" target="_blank">https://groups.google.com/d/msg/cp2k/-/u7HSXXG0XmMJ</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>.<br> </font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Chetan V Mahajan<br>PhD candidate, Ganesan Group<br>Department of Chemical Engineering<br>The University of Texas at Austin<br><br> </div></div></div>