Few questions from a beginner

[Chetan Mahajan]

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. 

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?

Thanks

Chetan

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Chetan V Mahajan
PhD candidate, Ganesan Group
Department of Chemical Engineering
The University of Texas at Austin

[Axel]

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.

[Chetan Mahajan]

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.

Thanks

Chetan

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