From owner-chemistry@ccl.net Fri Jan 17 10:12:00 2014 From: "Ajayakumar M R mr.ajay.mr{:}gmail.com" To: CCL Subject: CCL: Basic set selection Message-Id: <-49561-140117074244-8409-1KjQw7VC9mOo07P7Jrj21g-,-server.ccl.net> X-Original-From: "Ajayakumar M R" Date: Fri, 17 Jan 2014 07:42:43 -0500 Sent to CCL by: "Ajayakumar M R" [mr.ajay.mr(-)gmail.com] Dear all, I am not much familiar with computational chemistry and unable to understand many DFT/G09 technical terms. I was reading a paper and saw a calculation which was performed using with a 6-31+g(d) basis set for silicon, a 6-31+g(d) basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen atoms involved in bridging interactions. A 6-31g basis set was used for all remaining carbon and hydrogen atoms. my questions are, a) What is the difference between 6-31+g(d) vs 6-31+g(d)? b) How can we make the input file for these kind of calculations? c) What would be the reasons to select different basic sets for different atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? Looking for your kind responses. Thanking you, Dr. Ajayakumar, M. R. School of Physical Sciences Jawaharlal Nehru University New Delhi-110067 India From owner-chemistry@ccl.net Fri Jan 17 11:50:00 2014 From: "Utpal Sarkar utpalchemiitkgp- -gmail.com" To: CCL Subject: CCL: Basic set selection Message-Id: <-49562-140117114524-21414-A0iLeKsJZzubnwvWgbhxXg!^!server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Jan 2014 22:15:17 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp a gmail.com] a) What is the difference between 6-31+g(d) vs 6-31+g(d)? these two are same basis set. b) How can we make the input file for these kind of calculations? to use different basis set you can use GEN keyword in the route section and at the end of geometry section you can specify which basis set for which atom c) What would be the reasons to select different basic sets for different atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? because not same basis set is fit for all atoms. Here N,O etc you can use 'diffuse' and 'polarization' also along with 6-31+g(d). hope it will help best utpal On 1/17/14, Ajayakumar M R mr.ajay.mr{:}gmail.com wrote: > > Sent to CCL by: "Ajayakumar M R" [mr.ajay.mr(-)gmail.com] > Dear all, > > I am not much familiar with computational chemistry and unable to understand > > many DFT/G09 technical terms. I was reading a paper and saw a calculation > which was performed using with a 6-31+g(d) basis set for silicon, a > 6-31+g(d) > basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen atoms > involved in bridging interactions. A 6-31g basis set was used for all > remaining carbon and hydrogen atoms. > > my questions are, > > a) What is the difference between 6-31+g(d) vs 6-31+g(d)? > b) How can we make the input file for these kind of calculations? > c) What would be the reasons to select different basic sets for different > atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? > > Looking for your kind responses. > > Thanking you, > Dr. Ajayakumar, M. R. > School of Physical Sciences > Jawaharlal Nehru University > New Delhi-110067 > India> > > From owner-chemistry@ccl.net Fri Jan 17 12:25:00 2014 From: "Dr. Vitaly Chaban vvchaban:+:gmail.com" To: CCL Subject: CCL:G: Basic set selection Message-Id: <-49563-140117120913-30455-SvKBXgkL+JJVX8o0YDeVGg#%#server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Jan 2014 18:08:26 +0100 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban+*+gmail.com] > > I am not much familiar with computational chemistry and unable to understand > many DFT/G09 technical terms. I was reading a paper and saw a calculation > which was performed using with a 6-31+g(d) basis set for silicon, a 6-31+g(d) > basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen atoms > involved in bridging interactions. A 6-31g basis set was used for all > remaining carbon and hydrogen atoms. > > my questions are, > > a) What is the difference between 6-31g(d) vs 6-31+g(d)? The difference is in diffuse functions. See more about notations here: http://en.wikipedia.org/wiki/Basis_set_(chemistry) > b) How can we make the input file for these kind of calculations? I do not know if this trick is possible in Gaussian. > c) What would be the reasons to select different basic sets for different > atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? They probably want problems with BSSE... Most people would just run this system using 6-31+g(d) or aug-cc-pvDZ. I am afraid the selection of particular basis set is very much a matter of taste in modern ab initio calculations. Good luck, Dr. Vitaly V. Chaban > Looking for your kind responses. > > Thanking you, > Dr. Ajayakumar, M. R. > School of Physical Sciences > Jawaharlal Nehru University > New Delhi-110067 > India> > From owner-chemistry@ccl.net Fri Jan 17 13:00:00 2014 From: "Adam Tenderholt atenderholt~~gmail.com" To: CCL Subject: CCL:G: Basic set selection Message-Id: <-49564-140117124323-21116-6KbbKG065RsW1lMxhy2UxQ]^[server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=bcaec51b202997a2f504f02e13eb Date: Fri, 17 Jan 2014 09:42:53 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt,,gmail.com] --bcaec51b202997a2f504f02e13eb Content-Type: text/plain; charset=ISO-8859-1 I think Utpal's answers should be expanded upon a bit. a) What is the difference between 6-31+g(d) vs 6-31+g(d)? I think you probably meant the difference between 6-31+g(d) and 6-31g. Each basis set is of the 6-31G family, but the first basis set has an extra set of both polarization and diffuse functions on the atoms (except H and He). See the wikipedia page about basis sets. b) How can we make the input file for these kind of calculations? Do you mean for Gaussian 09? Or how do you make input files in general? If you're just starting out with calculations, I'd recommend Avogadro since it's open source and has input generators for a lot of QM pacakges. c) What would be the reasons to select different basic sets for different atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? In general, the energies for calculations become more accurate with the more functions in the basis set---so 6-31+g(d) is "better" than 6-31g. There are tons of basis sets, ranging from the very simple STO-3G to the very complex aug-cc-pV5Z. Note that more basis functions requires more CPU time, and depending on the DFT method, can scale as N^3 or N^4 (where N is the number of basis sets). So it's all about balancing quality of calculation and your computational resources. The general rules I learned years ago was that you should 1) always use polarization functions on heavy atoms, that is, the (d) part of the 6-31+g(d); 2) do optimizations and frequency calculations with double-zeta basis sets (e.g. 6-31G(d)), and 3) single point energy calculations should use triple-zeta basis sets (e.g. 6-311G(d)). I've also read that diffuse functions (the + part of your basis sets) should be used if you're calculating pKa's and such. Hope that helps, Adam On Fri, Jan 17, 2014 at 8:45 AM, Utpal Sarkar utpalchemiitkgp- -gmail.com < owner-chemistry,+,ccl.net> wrote: > > Sent to CCL by: Utpal Sarkar [utpalchemiitkgp a gmail.com] > a) What is the difference between 6-31+g(d) vs 6-31+g(d)? > > these two are same basis set. > > b) How can we make the input file for these kind of calculations? > > to use different basis set you can use GEN keyword in the route section > and at the end of geometry section you can specify which basis set for > which atom > > c) What would be the reasons to select different basic sets for different > atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? > > because not same basis set is fit for all atoms. Here N,O etc you can > use 'diffuse' and 'polarization' also along with 6-31+g(d). > hope it will help > best > utpal > > > On 1/17/14, Ajayakumar M R mr.ajay.mr{:}gmail.com > wrote: > > > > Sent to CCL by: "Ajayakumar M R" [mr.ajay.mr(-)gmail.com] > > Dear all, > > > > I am not much familiar with computational chemistry and unable to > understand > > > > many DFT/G09 technical terms. I was reading a paper and saw a calculation > > which was performed using with a 6-31+g(d) basis set for silicon, a > > 6-31+g(d) > > basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen > atoms > > involved in bridging interactions. A 6-31g basis set was used for all > > remaining carbon and hydrogen atoms. > > > > my questions are, > > > > a) What is the difference between 6-31+g(d) vs 6-31+g(d)? > > b) How can we make the input file for these kind of calculations? > > c) What would be the reasons to select different basic sets for different > > atoms? Why they did not perform a calculation with 6-31+g(d)for all > atoms? > > > > Looking for your kind responses. > > > > Thanking you, > > Dr. Ajayakumar, M. R. > > School of Physical Sciences > > Jawaharlal Nehru University > > New Delhi-110067 > > India> > > --bcaec51b202997a2f504f02e13eb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I think Utpal's answers should be expanded upon a bit.=

a)=A0What is the difference between =A06-31+g(d) vs 6-31+g(d)?

I think you probably meant the difference between 6-3= 1+g(d) and 6-31g. Each basis set is of the 6-31G family, but the first basi= s set has an extra set of both polarization and diffuse functions on the at= oms (except H and He). See the wikipedia page about basis sets.

b) How can we make the input file for these kind of calculations?

Do you= mean for Gaussian 09? Or how do you make input files in general? If you= 9;re just starting out with calculations, I'd recommend Avogadro since = it's open source and has input generators for a lot of QM pacakges.

c) What would be the reasons to select different basic sets for differe= nt
atoms? Why they did not perform a calculation with 6-31+g(d)for all ato= ms?

In general, the energies for cal= culations become more accurate with the more functions in the basis set---s= o 6-31+g(d) is "better" than 6-31g. There are tons of basis sets,= ranging from the very simple STO-3G to the very complex aug-cc-pV5Z. Note = that more basis functions requires more CPU time, and depending on the DFT = method, can scale as N^3 or N^4 (where N is the number of basis sets). So i= t's all about balancing quality of calculation and your computational r= esources.

The general rules I learned years ago was that you shou= ld 1) always use polarization functions on heavy atoms, that is, the (d) pa= rt of the 6-31+g(d); 2) do optimizations and frequency calculations with do= uble-zeta basis sets (e.g. 6-31G(d)), and 3) single point energy calculatio= ns should use triple-zeta basis sets (e.g. 6-311G(d)). I've also read t= hat diffuse functions (the + part of your basis sets) should be used if you= 're calculating pKa's and such.

Hope that helps,

Adam



On Fri, Jan 17, 2014 at 8:45 AM, Utpal Sarkar utpalchemiitkgp- -= gmail.com <owner-chemistry,+,ccl.net<= /a>> wrote:

Sent to CCL by: Utpal Sarkar [utpalchemiitkgp a gmail.com]
a) What is the difference between =A06-31+g(d) vs 6-31+g(= d)?

these two are same basis set.

b) How can we make the input file for these kind of calculations?

to use different basis set you can use GEN keyword in the route secti= on
and at the end of geometry section you can specify which basis set for
which atom

c) What would be the reasons to select different basic sets for different atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms?<= br>
because not same basis set is fit for all atoms. Here N,O etc you can=
use 'diffuse' and 'polarization' also along with 6-31+g(d).=
hope it will help
best
utpal


On 1/17/14, Ajayakumar M R = mr.ajay.mr{:}gmail.com
<owner-chemistry ~~ ccl.net> wrote:
>
> Sent to CCL by: "Ajayakumar =A0 M R" [mr.ajay.mr(-)gmail.com]
> Dear all,
>
> I am not much familiar with computational chemistry and unable to unde= rstand
>
> many DFT/G09 technical terms. I was reading a paper and saw a calculat= ion
> which was performed using with a 6-31+g(d) basis set for silicon, a > 6-31+g(d)
> basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen a= toms
> involved in bridging interactions. A 6-31g basis set was used for all<= br> > remaining carbon and hydrogen atoms.
>
> my questions are,
>
> a) What is the difference between =A06-31+g(d) vs 6-31+g(d)?
> b) How can we make the input file for these kind of calculations?
> c) What would be the reasons to select different basic sets for differ= ent
> atoms? Why they did not perform a calculation with 6-31+g(d)for all at= oms?
>
> Looking for your kind responses.
>
> Thanking you,
> Dr. Ajayakumar, M. R.
> School of Physical Sciences
> Jawaharlal Nehru University
> New Delhi-110067
> India>
>
>



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--bcaec51b202997a2f504f02e13eb-- From owner-chemistry@ccl.net Fri Jan 17 15:07:01 2014 From: "Errol Lewars elewars^-^trentu.ca" To: CCL Subject: CCL: Basic set selection Message-Id: <-49565-140117150354-4391-b72Rc6YnYsR4LuM0Ezoa5A ~~ server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 17 Jan 2014 15:04:04 -0500 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars[A]trentu.ca] 2014 Jan 17 (a) "What is the difference between 6-31+g(d) vs 6-31+g(d)?" I think you made a typo here. But for a reasonable explanation of the differences between various basis sets, read the chapter on ab initio calculations in some introduction to computational chemistry. Briefly, 6-31G lacks diffuse (+) and polarization (d) functions. 6-31G seems very unusual, compared to the popular 6-31G(d) (i.e. 6-31G*). (b) The exact nature of the input depends on the program being used. (c) One expects (but can't absolutely count on it) the best results from uniformly using the biggest basis you can "afford" (in time and computer resources). So a priori a 6-31+g(d)basis for all atoms would seem better than a 6-31G(d) on some atoms; presumably they could not afford the bigger basis on all the atoms. E.Lewars == Ajayakumar M R mr.ajay.mr{:}gmail.com wrote: > Sent to CCL by: "Ajayakumar M R" [mr.ajay.mr(-)gmail.com] > Dear all, > > I am not much familiar with computational chemistry and unable to understand > many DFT/G09 technical terms. I was reading a paper and saw a calculation > which was performed using with a 6-31+g(d) basis set for silicon, a 6-31+g(d) > basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen atoms > involved in bridging interactions. A 6-31g basis set was used for all > remaining carbon and hydrogen atoms. > > my questions are, > > a) What is the difference between 6-31+g(d) vs 6-31+g(d)? > b) How can we make the input file for these kind of calculations? > c) What would be the reasons to select different basic sets for different > atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? > > Looking for your kind responses. > > Thanking you, > Dr. Ajayakumar, M. R. > School of Physical Sciences > Jawaharlal Nehru University > New Delhi-110067 > India> > == Ajayakumar M R mr.ajay.mr{:}gmail.com wrote: > Sent to CCL by: "Ajayakumar M R" [mr.ajay.mr(-)gmail.com] > Dear all, > > I am not much familiar with computational chemistry and unable to understand > many DFT/G09 technical terms. I was reading a paper and saw a calculation > which was performed using with a 6-31+g(d) basis set for silicon, a 6-31+g(d) > basis set for oxygen, fluorine, nitrogen and all carbon and hydrogen atoms > involved in bridging interactions. A 6-31g basis set was used for all > remaining carbon and hydrogen atoms. > > my questions are, > > a) What is the difference between 6-31+g(d) vs 6-31+g(d)? > b) How can we make the input file for these kind of calculations? > c) What would be the reasons to select different basic sets for different > atoms? Why they did not perform a calculation with 6-31+g(d)for all atoms? > > Looking for your kind responses. > > Thanking you, > Dr. Ajayakumar, M. R. > School of Physical Sciences > Jawaharlal Nehru University > New Delhi-110067 > India> >