From owner-chemistry@ccl.net Sun Apr 10 02:26:01 2016 From: "Mehdi Esrafili m_esrafili-,-yahoo.com" To: CCL Subject: CCL:G: basis set augmented with bond-function Message-Id: <-52136-160410022501-31452-jur/QJqXPeUpciokx2/TaA]|[server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="----=_Part_157926_231393212.1460269494697" Date: Sun, 10 Apr 2016 06:24:54 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili=-=yahoo.com] ------=_Part_157926_231393212.1460269494697 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Dr. V=C3=ADctor Lua=C3=B1aThank you so much for your prompt reply. Bu= t, when I add the ghost atom (denoted as Bq atom) for the the middle of the= H...N bond of the optimized hydrogen-bonded FH...NCH complex, even using a= large base set located on the Bq atom, the total energy is not changed at = all. Also, the number of basis functions and primitive gaussians are also s= ame. Is there any special command in Gaussain for doing such calculations?= =C2=A0=20 With best regardsMehdi =C2=A0=C2=A0---------------------------------------------------------------= ---------------------------------------------------------------=C2=A0=C2=A0= `The man who makes no mistakes does not usually make anything.'=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Edward John Phelps (1822-1900)--------= ---------------------------------------------------------------------------= -------------------------------------------=20 Mehdi D. Esrafili, Ph.D.Assistant Professor of Physical Chemistry=C2=A0 Current address:=C2=A0Department of Chemistry, Faculty of Basic Sciences,Un= iversity ofMaragheh, Iran. E-mail 1: m_esrafili]|[yahoo.com=20 E-mail 2: esrafili]|[maragheh.ac.ir------------------------------------------= ---------------------------------------------------------------------------= --------- =20 On Sunday, April 10, 2016 4:03 AM, V=C3=ADctor Lua=C3=B1a Cabal victor!= =3D!fluor.quimica.uniovi.es wrote: =20 =20 Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor:+:f= luor.quimica.uniovi.es] On Sat, Apr 09, 2016 at 07:17:42PM +0000, Mehdi Esrafili m_esrafili]|[yahoo= .com wrote: > Dear all;I have a question about how I can do a single point > calculation with basis set augmented with so called bond-function > in Gaussian 09?Any idea/suggestion is greatly appreciated.With best > regardsMehdi Mehdi, You can define a ghost atom in the middle of the bond and associate a basis set to that atom. The idea is simple. In fact, you can use this trick to define a collection of charges and multipoles forming an embedding for the central atom or cluster of your election. Good luck, =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a -- =C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "In science a person can be convinced = by a good argument. =C2=A0 =C2=A0 / `' \=C2=A0 That is almost impossible in politics or religio= n" =C2=A0 /(o)(o)\=C2=A0 (Adapted from Carl Sagan) =C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero tambi=C3=A9= n es peor /=C2=A0 '`'`=C2=A0 \ que lo malo, porque la mediocridad no es un grado, es= una |=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015 |=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it is also worse = than =C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade, it is an at= titude) =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"la religi=C3=B3n e= s verdadera para ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !los pobres, fa= lsa para los sabios, ! Universidad de Oviedo, 33006-Oviedo, Spain !y =C3=BAtil para los l=C3=ADd= eres"=C2=A0 =C2=A0=20 ! e-mail:=C2=A0 victor=3Dfluor.quimica.uniovi.es=C2=A0 !=C2=A0 =C2=A0 =C2= =A0 (Lucius Ann=C3=A6us Seneca) ! phone: +34-985-103491=C2=A0 fax: +34-985-103125 !"Religion is truth for t= he poor, +--------------------------------------------+false for the wise, and usefu= l GroupPage: http://azufre.quimica.uniovi.es/ for the leaders" -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------=_Part_157926_231393212.1460269494697 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Dr. V=C3=ADctor= Lua=C3=B1a
Thank you so much for = your prompt reply. But, when I add the ghost atom (denoted as Bq ato= m) for the the middle of the H...N bond of the optimized hydrogen-bonded FH= ...NCH complex, even using a large base set located on the Bq atom, the tot= al energy is not changed at all. Also, the number of basis functions and pr= imitive gaussians are also same. Is there any special command in Gaussain f= or doing such calculations? 
With best regards
Mehdi
 
 
----------------------------------------------= ---------------------------------------------------------------------------= -----  
`The man who makes no mistakes does = not usually make anything.'
    &n= bsp;            = ;            &n= bsp;    Edward John Phelps (1822-1900)
-------------------------------------------------------------------------= -----------------------------------------------------
Mehdi D. Esrafili= , Ph.D.
Assistant Professor of Physical Chemistry = ;
Current address:&nb= sp;Department of Chemistry,
Faculty of Basic Sciences= ,University of
Maragheh, Iran.
E= -mail 1: m_esrafili]|[= yahoo.com
E-mail 2: esrafili]|[maragheh.ac.ir
---------------------------------------------------------= ---------------------------------------------------------------------


On Sunday, April 10, 2016 4:03 AM, V=C3=ADctor Lua=C3=B1a Cabal= victor!=3D!fluor.quimica.uniovi.es <owner-chemistry]|[ccl.net> wrote:<= br>



Sent to CCL b= y: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor:+:fluor.quimica.= uniovi.es]
On Sat, Apr 09, 2016 at 07:17:42PM +0000, Mehdi Esrafili m_es= rafili]|[yahoo.com wrote:
> Dear all;I have a question about how I ca= n do a single point
> calculation with basis set augmented with so ca= lled bond-function
> in Gaussian 09?Any idea/suggestion is greatly ap= preciated.With best
> regardsMehdi

Mehdi,

You can defin= e a ghost atom in the middle of the bond and associate
a basis set to th= at atom. The idea is simple. In fact, you can use
this trick to define a= collection of charges and multipoles forming an
embedding for the centr= al atom or cluster of your election.

Good luck,
    &nb= sp;     Dr. V=C3=ADctor Lua=C3=B1a
--
    .&nbs= p; .    "In science a person can be convinced by a good argument.=
    / `' \  That is almost impossible in politics or re= ligion"
  /(o)(o)\  (Adapted from Carl Sagan)
  /`. \= / .'\  "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peor /  '`'`  \ que lo malo, porque la mediocridad no es un grado,= es una
|  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
|&= nbsp; |'`'`|  | (Mediocre is worse than good, but it is also worse tha= n
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is = an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! = Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"la religi=C3=B3n= es verdadera para
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3= =ADtica !los pobres, falsa para los sabios,
! Universidad de Oviedo, 330= 06-Oviedo, Spain !y =C3=BAtil para los l=C3=ADderes"   
! e-= mail:  victor=3Dfluor.quimica.uniovi.es  !      = (Lucius Ann=C3=A6us Seneca)
! phone: +34-985-103491  fax: +34-985-1= 03125 !"Religion is truth for the poor,
+-------------------------------= -------------+false for the wise, and useful
GroupPage: http://azufre.quimica.uniov= i.es/ for the leaders"



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------=_Part_157926_231393212.1460269494697-- From owner-chemistry@ccl.net Sun Apr 10 19:43:01 2016 From: "Susi Lehtola susi.lehtola+/-alumni.helsinki.fi" To: CCL Subject: CCL:G: basis set augmented with bond-function Message-Id: <-52137-160410173325-3502-rs7D0gVsAKtJpWzYRgzxSQ-*-server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sun, 10 Apr 2016 14:33:11 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola- -alumni.helsinki.fi] On 04/09/2016 11:24 PM, Mehdi Esrafili m_esrafili-,-yahoo.com wrote: > Dear Dr. Víctor Luaña Thank you so much for your prompt reply. But, > when I add the ghost atom (denoted as Bq atom) for the the middle of > the H...N bond of the optimized hydrogen-bonded FH...NCH complex, > even using a large base set located on the Bq atom, the total energy > is not changed at all. Also, the number of basis functions and > primitive gaussians are also same. Is there any special command in > Gaussain for doing such calculations? With best regards Mehdi Dear Mehdi, I bet you did not specify basis functions for the ghost atom. Gaussian has a nasty way of running calculations even if you forget to specify basis functions for some center. This must be the case, if the number of basis functions did not change. It is hard to find the problem if you don't attach an input file, please do so the next time... -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola:+:alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------