[CP2K:3718] Re: Few questions from a beginner

Chetan Mahajan cheta... at gmail.com
Wed Jan 25 03:59:11 UTC 2012

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.


On Tue, Jan 24, 2012 at 9:42 PM, Axel <akoh... at gmail.com> wrote:

> On Tuesday, January 24, 2012 10:02:34 PM UTC-5, Chetan Mahajan wrote:
>> Hello Friends
>> 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:
>> 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.
> the cramer book is very "essential" and does not touch a lot of what is
> relevant for cp2k.
> a lot of the "slang" related to cp2k comes from the condensed matter
> physics / electronic
> structure area and is best understood, if you also gain some understanding
> of pure
> plane wave basis set DFT calculations (e.g. in the form of car-parrinello
> MD).
> a good introduction that is palatable for people with a chemistry training
> (there are
> other good ones, but they are more accessible to people with a strong
> physics
> background), is in my opinion "electronic structure calculations for solid
> and molecules:
> theory and computational methods" by jorge kohanoff.
> from there on, you can work your way through some of the cp2k papers
> and more specific books. as a rule of the thumb you should keep in mind
> that the integral of all evil things remains a constant, i.e. for every
> benefit
> there is a disadvantage. which means, that you have to expect to make
> some serious mistakes until you get to know those problems. it is
> therefore highly recommended to not start with something too difficult
> or too complex. that will just increase the number of possibilities for
> errors and decrease the chances to detect them.
>> 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?
> this is very difficult to say without knowing the exact difference between
> your equilibrated and non-equilibrated system. do they have the same
> volume? are they both neutral?  if the difference is rather small, it can
> just
> be that what is equilibrated with a classical model has some too close
> contacts for your DFT calculation. also keep in mind that (simple) DFT
> (e.g. BLYP) is notoriously bad at representing dispersion interactions.
> it could also just mean that you may not have converged one of the
> wavefunctions to the real ground state. there are many things that
> can go wrong and it is difficult judge only from the total energy.
> axel.
>> Thanks
>> Chetan
>> --
>> Chetan V Mahajan
>> PhD candidate, Ganesan Group
>> Department of Chemical Engineering
>> The University of Texas at Austin
>>   --
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Chetan V Mahajan
PhD candidate, Ganesan Group
Department of Chemical Engineering
The University of Texas at Austin
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