From owner-chemistry@ccl.net Tue Feb 26 02:07:00 2013 From: "Jean Jules Fifen julesfifen .. gmail.com" To: CCL Subject: CCL:G: calcfc Gaussian 09 Message-Id: <-48316-130226020438-1138-3DqbwPzFkhsncOBW1pd5Qw/a\server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: multipart/alternative; boundary=90e6ba6e8b50ef157604d69b44bf Date: Tue, 26 Feb 2013 08:04:31 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen{}gmail.com] --90e6ba6e8b50ef157604d69b44bf Content-Type: text/plain; charset=ISO-8859-1 What I can say is that, You can use this option when simple optimizations do not converge. The main drawback of using this keyword is the CPU time consuming. On 25 February 2013 14:49, Raphael Martinez raphaelmartinez1983###gmail.com wrote: > > Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983**gmail.com] > Hello everyone: > I have a very basic/quick question. I am using Gaussian 09. > I know that using the option "calcfc" in the optimization is a bit > expensive. So, I have few questions > about it: > 1. I was wondering if this option "calcfc" must be always use in the > optimizations, or I can avoid it? > 2. If I avoid the "calcfc", am I going to obtain a bad optimization? > 3. are there certain cases in which is better to use it and cases in which > I can avoid it? > > Thank you all for the help > > Raphael> > > -- *J. Jules Fifen.* --90e6ba6e8b50ef157604d69b44bf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
What I can say is that,
You can use this option when simple optimizations do not converge. The = main drawback of using this keyword is the CPU time consuming.


O= n 25 February 2013 14:49, Raphael Martinez raphaelmartinez1983###gmail.com <owner-chemistry:+:ccl.net> wrote:

Sent to CCL by: "Raphael =A0Martinez" [raphaelmartinez1983**gmail.com]
Hello everyone:
I have a very basic/quick question. I am using Gaussian 09.
I know that using the option "calcfc" in the optimization is a bi= t expensive. So, I have few questions
about it:
1. I was wondering if this option "calcfc" must be always use in = the optimizations, or I can avoid it?
2. If I avoid the "calcfc", am I going to obtain a bad optimizati= on?
3. are there certain cases in which is better to use it and cases in which = I can avoid it?

Thank you all for the help

Raphael



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--
J. Jules Fifen.
--90e6ba6e8b50ef157604d69b44bf-- From owner-chemistry@ccl.net Tue Feb 26 08:06:01 2013 From: "MOREAU Yohann 224609 yohann.moreau]=[cea.fr" To: CCL Subject: CCL:G: calcfc Gaussian 09 Message-Id: <-48317-130226070233-20444-zAdjEACBTo0V+PcSlIc/vw=server.ccl.net> X-Original-From: MOREAU Yohann 224609 Content-Language: fr-FR Content-Type: multipart/alternative; boundary="_000_434E55F17127E545B1D13ED19A1BFD522D30722FEXDAG0B1intrace_" Date: Tue, 26 Feb 2013 12:02:23 +0000 MIME-Version: 1.0 Sent to CCL by: MOREAU Yohann 224609 [yohann.moreau-,-cea.fr] --_000_434E55F17127E545B1D13ED19A1BFD522D30722FEXDAG0B1intrace_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Raphael, In complement to Jean-Jules's answer I'd add this: calcfc is an option that calculate the full hessian matrix (second derivati= ves of the energy with respect to nuclear coordinates) for your system. As = previously mentioned, It can be very cpu-time/memory consuming. Here are some answers to your questions: 1- No. You only rarely need to start by calculating force constants, at least when= optimizing a system toward a minimum of the PES. By default, Gaussian estimates the force constants (eq. to opt=3Dnewestmfc= ) that will be used in the minimization algorithm at the beginning (with a = valence force field, which is not time consuming). Furthermore, along the o= ptimization, the hessian matrix is updated. 2nd derivatives are used in met= hods such as ones based on Newton-Raphson approach, e.g. 2- Same answer as above but with a precision: for a minimum search, things = happen generally well, in most of the cases, calcfc is not needed. When you are looking for a transition state, things are different: you have= to provide a proper hessian matrix (see Gaussian User's manual for TS sear= ch, which can be a tricky task, sometimes), which means that either you pro= vide it from a previous calculation or calculate it with calcfc. 3- Almost a linear combination of the two previous answers: When looking for a minimum, the use of calcfc is rarely (even almost never)= needed. But when looking for a TS, this is needed if you don't provide the= hessian from a previous calculation. To finish, I absolutely want to "modulate" my answers: every chemical syste= m is particular and will behave a particular way. Hence, the calculation of= the hessian matrix before a minimum search could be needed, as already wri= tten by Jean-Jules. I hope this clarified things. Anyway,I suggest you to have a look at Gaussian09 User's reference, especi= ally: http://www.gaussian.com/g_tech/g_ur/k_opt.htm which describes very pr= ecisely the use of different keywords related to optimization methods. I wo= uld also suggest some further readings about optimization techniques and al= gorithms like in chapter 12 (p380, 2nd edition) of F. Jensen's "Introductio= n to Computational Chemistry" or section 4 of chapter 2 (pp 40-46) in C. C= ramer's Book: "Essentials of Computational Chemistry". Best Regards, Yohann -- Yohann Moreau Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier iRTSV/CBM/MCT, CEA Grenoble 17 avenue des Martyrs 38 054 Grenoble Cedex 09 Tel. : (33) 4 38 78 29 62 Fax : (33) 4 38 78 54 87 De : "Jean Jules Fifen julesfifen .. gmail.com" > R=E9pondre =E0 : CCL Subscribers > Date : mardi 26 f=E9vrier 2013 08:04 =C0 : MOREAU Yohann 224609 > Objet : CCL:G: calcfc Gaussian 09 What I can say is that, You can use this option when simple optimizations do not converge. The main= drawback of using this keyword is the CPU time consuming. On 25 February 2013 14:49, Raphael Martinez raphaelmartinez1983###gmail.com= > wrote: Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983**gmail.com] Hello everyone: I have a very basic/quick question. I am using Gaussian 09. I know that using the option "calcfc" in the optimization is a bit expensiv= e. So, I have few questions about it: 1. I was wondering if this option "calcfc" must be always use in the optimi= zations, or I can avoid it? 2. If I avoid the "calcfc", am I going to obtain a bad optimization? 3. are there certain cases in which is better to use it and cases in which = I can avoid it? Thank you all for the help Raphael -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY[*]ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST[*]ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- J. Jules Fifen. --_000_434E55F17127E545B1D13ED19A1BFD522D30722FEXDAG0B1intrace_ Content-Type: text/html; charset="iso-8859-1" Content-ID: <862D7BA090315F48A2EFE908372FCB4B,cea.fr> Content-Transfer-Encoding: quoted-printable
Dear Raphael, 

In complement to Jean-Jules's answer I= 'd add this: 

calcfc is an option that calculate the= full hessian matrix (second derivatives of the energy with respect to nucl= ear coordinates) for your system. As previously mentioned, It can be very c= pu-time/memory consuming.

Here are some answers to your question= s:

1- No. 
You only rarely need to start by calculating force constants, at least= when optimizing a system toward a minimum of the PES. 
By default, Gaussian estimates the for= ce constants (eq. to  opt=3Dnewestmfc) that will be used in the minimi= zation algorithm at the beginning (with a valence force field, which is not= time consuming). Furthermore, along the optimization, the hessian matrix is updated. 2nd derivatives are used in m= ethods such as ones based on Newton-Raphson approach, e.g.

2- Same answer as above but with a pre= cision: for a minimum search, things happen generally well, in most of the = cases, calcfc is not needed.
When you are looking for a transition = state, things are different: you have to provide a proper hessian matrix (s= ee Gaussian User's manual for TS search, which can be a tricky task, someti= mes), which means that either you provide it from a previous calculation or calculate it with calcfc.

3- Almost a linear combination of the = two previous answers:
When looking for a minimum, the use of= calcfc is rarely (even almost never) needed. But when looking for a TS, th= is is needed if you don't provide the hessian from a previous calculation.<= /div>

To finish, I absolutely want to "= modulate" my answers: every chemical system is particular and will beh= ave a particular way. Hence, the calculation of the hessian matrix before a= minimum search could be needed, as already written by Jean-Jules.

I hope this clarified things. 

Anyway,I suggest you to  have a l= ook at Gaussian09 User's reference, especially: http://www.gaussian.com/g_tech/g_ur/k_o= pt.htm which describes very precisely the use of different keywords related to optimization methods. I would al= so suggest some further readings about optimization techniques and algorith= ms like in chapter 12 (p380, 2nd edition) of F. Jensen's "Introduction= to Computational Chemistry"  or section 4 of chapter 2 (pp 40-46) in C. Cramer's Book: "Essentials of Computati= onal Chemistry".

Best Regards, 

Yohann



-- 

Yohann Moreau

Ma=EEtre de Conf=E9rence, Universit=E9 Joseph Fourier
iRTSV/CBM/MCT, CEA Grenoble
17 avenue des Martyrs
38 054 Grenoble Cedex 09
Tel. : (33) 4 38 78 29 62
Fax : (33) 4 38 78 54 87

De : "Jean Jules Fifen ju= lesfifen .. gmail.com" <= owner-chemistry,ccl.net>
R=E9pondre =E0 : CCL Subscribe= rs <chemistry,ccl.net>
Date : mardi 26 f=E9vrier 2013= 08:04
=C0 : MOREAU Yohann 224609 <= ;yohann.moreau,cea.fr>
Objet : CCL:G: calcfc Gaussian= 09

What I can say is that,
You can use this option when simple optimizations do not converge. The main= drawback of using this keyword is the CPU time consuming.


On 25 February 2013 14:49, Raphael Martinez raph= aelmartinez1983###gmail.com<owner= -chemistry[*]ccl.net> wrote:

Sent to CCL by: "Raphael  Martinez" [raphaelmartinez1983**gmail.com]
Hello everyone:
I have a very basic/quick question. I am using Gaussian 09.
I know that using the option "calcfc" in the optimization is a bi= t expensive. So, I have few questions
about it:
1. I was wondering if this option "calcfc" must be always use in = the optimizations, or I can avoid it?
2. If I avoid the "calcfc", am I going to obtain a bad optimizati= on?
3. are there certain cases in which is better to use it and cases in which = I can avoid it?

Thank you all for the help

Raphael



-=3D This is automatically added to each message by the mailing script =3D-=
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--
J. Jules Fife= n.
--_000_434E55F17127E545B1D13ED19A1BFD522D30722FEXDAG0B1intrace_-- From owner-chemistry@ccl.net Tue Feb 26 08:40:00 2013 From: "David A Case case() biomaps.rutgers.edu" To: CCL Subject: CCL: Database of solvation energies Message-Id: <-48318-130225195327-28448-G7aEdvYJW/S6upKrB78eDA/./server.ccl.net> X-Original-From: David A Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 25 Feb 2013 19:54:10 -0500 Mime-Version: 1.0 Sent to CCL by: David A Case [case : biomaps.rutgers.edu] On Mon, Feb 25, 2013, Ramon Crehuet rcsqtc%iqac.csic.es wrote: > > I would like to get the *experimental* solvation energy (in water) of > HPO4^(2-) and HAsO4^(2-) (I want to compare with calculated values). I > can deduce those from the solvation energies of H3PO4 and H3AsO4 and > their pKa or from similar thermodynamic cycles. However, I looked for > both sets of data and couldn't find anything! We recently made a stab at collecting these for phosphoric acid: Steinbrecher, Latzer, Case, J Chem. Theory Comput. 8:4405, 2012, see esp. Table 6. But it's hard to make secure comparisons between experiment and theory, for the reasons discussed in the paper. ...dave case From owner-chemistry@ccl.net Tue Feb 26 10:51:00 2013 From: "mahnaz ghiasi mahnaz271163[A]yahoo.com" To: CCL Subject: CCL:G: how to define symmetry, thank you J. Message-Id: <-48319-130226104943-12902-1U52jl18zZpD/I4U4o7SQQ.:.server.ccl.net> X-Original-From: mahnaz ghiasi Content-Type: multipart/alternative; boundary="-2068959492-541504927-1361893774=:61555" Date: Tue, 26 Feb 2013 07:49:34 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: mahnaz ghiasi [mahnaz271163_-_yahoo.com] ---2068959492-541504927-1361893774=:61555 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable thank you J. =0AI was exactly looking what you said.=0A=A0Wish you increasi= ng ever success=0A=0A=0A=0A=0A________________________________=0A From: Jan= a Mathauserov=E1 jahodovykomplot__gmail.com =0ATo:= "Ghiasi, Mahnaz " =0ASent: Monday, Februa= ry 25, 2013 3:04 PM=0ASubject: CCL:G: how to define symmetry=0A =0A=0AI am = not sure what you are asking either, if you are just looking for a Gaussian= input keyword, it's symm(pg=3Dc2v)=0Afor the input line. You can also 'loc= k' some parameters (such as angles or dihedrals etc) by adding modredundant= ..=0A=0AJ.=0A=0A=0AOn 23 February 2013 21:54, mahnaz gh mahnaz271163!A!yaho= o.com wrote:=0A=0A=0A>Sent to CCL by: "mahnaz = =A0gh" [mahnaz271163() yahoo.com]=0A>I'd like to enquire about how I should= define a specific symmetry for my molecule (ligand).=0A>Please help me to = know what is the right keyword, my symmetry is C2V.=0A>where should I input= the keyword?=0A>=0A>mahnaz=0A>=0A>=0A>=0A>-=3D This is automatically added= to each message by the mailing script =3D-=0A>=0A>E-mail to subscribers: C= HEMISTRY#%#ccl.net or use:=0A>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/se= nd_ccl_message=0A>=0A>E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net= or use=0A>=A0 =A0 =A0=0A>= =0A>Subscribe/Unsubscribe:=0A>=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_= unsub.shtml=0A>=0A= =0A>=0A>Job: http://www.ccl.net/jobs=0A>Conferences: http://server.ccl.net/= chemistry/announcements/conferences/=0A>=0A>Search Messages: http://www.ccl= .net/chemistry/searchccl/index.shtml=0A>=0A>=A0 =A0 =A0 http://www.ccl.net/= spammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/aboutccl/instruction= s/=0A>=0A>=0A>=0A=0A=0A-- =0A=0A---=0AS pozdravem=0AJana Mathauserov=E1=0A= =0A+420 606 301 164=0A+44 079 79 217 846 ---2068959492-541504927-1361893774=:61555 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
thank you J.
I was exactly= looking what you said.
 Wish you increasing ever success
<= span>


From: Jana Mathauserov=E1 jahodovykomplot__gmail.com &l= t;owner-chemistry:+:ccl.net>
To:= "Ghiasi, Mahnaz " <mahnaz271163:+:yahoo.com>
<= b>Sent: Monday, February 25, = 2013 3:04 PM
Subject: = CCL:G: how to define symmetry

=0A
I am not sure what you are asking either, if you are just looking for= a Gaussian input keyword, it's symm(pg=3Dc2v)
for the input line. You c= an also 'lock' some parameters (such as angles or dihedrals etc) by adding = modredundant..
=0A
J.

O= n 23 February 2013 21:54, mahnaz gh mahnaz271163!A!yahoo.com &l= t;owner-chemistry#%#ccl= .net> wrote:
=0A

=0ASent to CCL by: "mahnaz  gh" [mahnaz271163= () yahoo.c= om]
=0AI'd like to enquire about how I should define a specific symm= etry for my molecule (ligand).
=0APlease help me to know what is the rig= ht keyword, my symmetry is C2V.
=0Awhere should I input the keyword?
= =0A
=0Amahnaz
=0A
=0A
=0A
=0A-=3D This is automatically adde= d to each message by the mailing script =3D-
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--

--= -
S pozdravem
Jana Mathauserov=E1

+420 606 301 164
+44 079 = 79 217 846
=0A


---2068959492-541504927-1361893774=:61555-- From owner-chemistry@ccl.net Tue Feb 26 23:43:00 2013 From: "Zheng Xu zjuxuzheng||gmail.com" To: CCL Subject: CCL: The benchmark method for predicting properties of Si-O-Si compounds? Message-Id: <-48320-130226232424-10010-9iQ6bxCvAiUmby904AEr1w[A]server.ccl.net> X-Original-From: "Zheng Xu" Date: Tue, 26 Feb 2013 23:24:23 -0500 Sent to CCL by: "Zheng Xu" [zjuxuzheng]=[gmail.com] Dear CCLs, I want to know certain properties for compounds including SiOSi linkage. The linearization energy for Si-O-Si was reported to be quite low (<0.5 kca/mol). A lot of theoretical methods can not give reasonable result for it's geometry. So I want to check whether a set of DFTs method are suitable for predicting the structure and intermolecular interactions involved by compounds that include Si-O-Si linkage. However, I am not sure which kind of methods can be used as the standards to evaluate their performance. The result of MP2 method in combination with large basis set is normally choosed as benchmark. Howevere, I found that MP2/aug-cc-pVQZ seems apparently overestimate the complexation energy. Is their lies any other choice? Does high-level composite procedures such as G3, CBS-QB3 and W1 can be used as the standards?